Unable to root using Flashtool 0.9.9.0 - XPERIA X10 Q&A, Help & Troubleshooting

My phone was already rooted using flashtool using 0.2.9.1 GB-ready and had unlocked bootloader. However on updating flashtool, the app tells me that my phone isn't rooted and doesn't have an unlocked bl as well. So I tried flashing it but every time I boot the device into flash mode the process stops and I get this error :
15/022/2012 19:22:13 - INFO - Please connect your device into flashmode.
15/022/2012 19:22:19 - INFO - Device connected in flash mode
15/022/2012 19:22:19 - INFO - Opening device for R/W
15/022/2012 19:22:19 - INFO - Reading device information
15/022/2012 19:22:19 - INFO - Phone ready for flashmode operations.
15/022/2012 19:22:19 - INFO - Start Flashing
15/022/2012 19:22:19 - INFO - Processing loader
15/022/2012 19:22:19 - INFO - Checking header
15/022/2012 19:22:19 - INFO - Ending flash session
15/022/2012 19:22:19 - ERROR - ERR_SEVERITY="MAJOR";ERR_CLASS="SECURITY_CLASS";ERR_DYNAMIC="SIN header verification failed"
Click to expand...
Click to collapse
Can anybody tell me the solution for this? I had xrecovery installed previously, I tried using SuperOneClick 2.3.3. Funny thing is that I can root my phone(shell root as well) and then start Flashtool 0.9.9 which will detect my phone as rooted(!).. but I can't install CWM recovery.. everytime I do so I get a process done message but if I go into Tools->Reboot->Recover->Specific Recovery all I get is a blank screen.
Now if I restart my phone after getting it rooted from superoneclick, it gets unrooted automatically! This is getting very confusing.. Can somebody help me please?

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OP sorry, I have no answers, but I have the same/similar problem.
I figure if I add my information to the information you have provided we may collectively invite some comment to stair us in the direction to an answer.
OP, hope that's OK with you.
Just one thing OP, have you installed the Flashtool 0.9.9 Windows update/bug fix (assuming you're using windows)??
FlashTool-windows-0.9.9update1.zip
I am having all sorts of problems attempting to install a CM9/CM10 kernel with CWM recovery mode on my XPERIA X10i.
My end goal is to install [CM10] v4 (Torch) by: scritch007
I have an unlock??? bootloader and can root my phone. But I'm beginning to question that!!!
I have the following information provided from S1 Tool
Code:
Welcome to S1 tool.
RUNNING S1_EROM VER "R8A031"
SOFTWARE AID: 0001
LOADER AID: 0001
FLASH ID: "002C/00B3"
LOADER VERSION: "R4A024"
MODEL (from GDFS): X10i
SOFTWARE VERSION: 1227-4612_3.0.1.G.0.75
CUSTOM VERSION: 1241-1846_R1C
FILESYSTEM VERSION: WORLD-1-4-8_3.0.1.G.0.75
SERIAL NO: CB537QU1MN
SEMC SIMLOCK CERTIFICATE
Elapsed:55 secs.
Using the service information menu *#*#7378423#*#* I was able to see my SIM lock was unlocked [] SIM = 0
I have installed a fresh copy of GB 2.3.3 using Flashtool 0.9.9 with additional Windows update1.
I used a 'World' GB 2.3.3 ftf see above.
I have also installed GB using Sony Ericsson Update Service (SEUS) which provides the same base OS.
[Root XPERIA X10i using FlashTool 0.9.9]
I have rooted the device using ZergRush exploit from Flashtools 0.9.9 with update patch FlashTool-windows-0.9.9update1.zip
To do this, I started the phone and enabled debug and unknown source.
With the phone still up and running and Flashtool 0.9.9 also running, I plugged in the USB cable.
I select the "My X10" option -> root -> Force ZergRush and the process then rooted the phone and the phone rebooted with root access, no problems there.
Code:
19/042/2012 11:42:06 - INFO - <- This level is successfully initialized
19/042/2012 11:42:06 - INFO - Flashtool Version 0.9.9.0 built on 2012-11-21 23:15:59
19/042/2012 11:42:06 - INFO - You can drag and drop ftf files here to start flashing them
19/042/2012 11:42:12 - INFO - Device connected with USB debugging on
19/042/2012 11:42:12 - INFO - Connected device : X10
19/042/2012 11:42:12 - INFO - Installed version of busybox : BusyBox v1.15.3 (2010-02-06 17:13:19 CET) multi-call binary
19/042/2012 11:42:12 - INFO - Android version : 2.3.3 / kernel version : 2.6.29-modFXP-DooMKernel-v06 / Build number : 3.0.1.G.0.75
19/042/2012 11:42:12 - INFO - Root Access Allowed
I can also install CWM recovery this way too.
After I have gained root access I have the phone up and running and again plug the USB cable in.
I select recovery mode option in Flashtool 0.9.9 and I'm requested to power down my phone and reconnect.
This then installs a recovery mode, either CWM or xRecovery depending on which one I select.
Again, this is all good and I can boot into either xRecovery or CWM recovery depending on which is installed.
I have installed and used other versions of Flashtool, however the outcomes always seems to be the same.
If I attempt to install a CM9/CM10 ftf I get the following error message:
Code:
19/016/2012 03:16:36 - INFO - <- This level is successfully initialized
19/016/2012 03:16:36 - INFO - Flashtool Version 0.9.9.0 built on 2012-11-21 23:15:59
19/016/2012 03:16:36 - INFO - You can drag and drop ftf files here to start flashing them
19/016/2012 03:16:42 - INFO - Device disconnected
19/016/2012 03:16:55 - INFO - Selected X10_4.1.X_CMX10_bootmanager_v14.ftf
19/016/2012 03:16:55 - INFO - Preparing files for flashing
19/016/2012 03:16:56 - INFO - Please connect your device into flashmode.
19/017/2012 03:17:45 - INFO - Device connected in flash mode
19/017/2012 03:17:46 - INFO - Opening device for R/W
19/017/2012 03:17:46 - INFO - Reading device information
19/017/2012 03:17:46 - INFO - Phone ready for flashmode operations.
19/017/2012 03:17:46 - INFO - Start Flashing
19/017/2012 03:17:46 - INFO - Processing loader
19/017/2012 03:17:46 - INFO - Checking header
19/017/2012 03:17:46 - INFO - Ending flash session
19/017/2012 03:17:46 - ERROR - ERR_SEVERITY="MAJOR";ERR_CLASS="SECURITY_CLASS";ERR_DYNAMIC="SIN header verification failed"
19/017/2012 03:17:46 - ERROR - Error flashing. Aborted
19/017/2012 03:17:46 - INFO - Device connected in flash mode
19/017/2012 03:17:47 - INFO - Device disconnected
19/017/2012 03:17:49 - INFO - Device connected in flash mode
19/018/2012 03:18:10 - INFO - Device disconnected
19/018/2012 03:18:13 - INFO - Device connected with USB debugging off
19/018/2012 03:18:13 - INFO - For 2011 devices line, be sure you are not in MTP mode
19/018/2012 03:18:23 - INFO - Device disconnected
At the moment I have just given up until I have some good leads to renew my CM9/CM10 install efforts.
At the moment I have GB 2.3.3 rooted with ZergRush exploit.
xRecovery installed
DooMLoRD DooMkernel V6 install with overclocked CPU of 1152MHz
The phone is up and running, rooted and has a modified Kernel which I recovered via xRecovery backup restore.
So, I have a working GB 2.3.3 phone with root access....but I want more...
My phone seems to be a one trick pony and I don't seem to be able to install CM9/CM10 with the information I have to hand.
Any thoughts I why I'd be getting the "SIN header verification failed" message????
********* Update **************
[ANSWER]
I solved my problem by unlocking the bootloader on my XPERIA X10i using the following information.
Tutorial: Rooting, Bootloader unlocking&updating
Remember to have debugging and Unknown source ticked on your XPERIA X10i phone.
Code:
20/015/2012 16:15:44 - INFO - Device connected with USB debugging off
20/015/2012 16:15:44 - INFO - For 2011 devices line, be sure you are not in MTP mode
20/015/2012 16:15:44 - INFO - Device connected with USB debugging on
20/015/2012 16:15:45 - INFO - Connected device : X10
20/015/2012 16:15:45 - INFO - Installed version of busybox : BusyBox v1.19.0 (2011-08-14 23:46:58 CDT) multi-call binary.
20/015/2012 16:15:45 - INFO - Android version : 2.3.3 / kernel version : 2.6.29-00054-g5f01537
20/015/2012 16:15:46 - INFO - Remounting system read-write
20/015/2012 16:15:46 - INFO - Installing toolbox to device...
20/015/2012 16:15:46 - INFO - Pushing C:\Program Files\Flashtools 0.8.6\Flashtool\custom\root\ftkit.tar to /data/local/tmp
20/015/2012 16:15:46 - INFO - Running installftkit as root thru sysrun
20/015/2012 16:15:47 - INFO - Root Access Allowed
20/016/2012 16:16:22 - INFO - Please connect your device into flashmode.
20/016/2012 16:16:27 - INFO - Device disconnected
20/017/2012 16:17:22 - INFO - Device connected in flash mode
20/017/2012 16:17:22 - INFO - Opening device for R/W
20/017/2012 16:17:22 - INFO - Reading device information
20/017/2012 16:17:22 - INFO - Phone ready for flashmode operations.
20/017/2012 16:17:22 - INFO - Flashing loader
[COLOR="Red"]20/017/2012 16:17:24 - INFO - Loader : S1_Loader_Root_f851 - Version : R4A024 / Bootloader status : UNROOTABLE[/COLOR]
20/017/2012 16:17:24 - INFO - Start Reading property
20/017/2012 16:17:24 - INFO - Reading TA finished.
20/017/2012 16:17:24 - INFO - Ending flash session
20/017/2012 16:17:24 - INFO - Found semcSL
20/017/2012 16:17:24 - INFO - You can now unplug and turn on device, then plug it again
20/017/2012 16:17:24 - INFO - Waiting for device
20/019/2012 16:19:39 - INFO - Device connected with USB debugging on
20/019/2012 16:19:40 - INFO - Pushing C:\Program Files\Flashtools 0.8.6\Flashtool\custom\features\UnlockBL\files\qsd8250\qsd8250bootwrite_semcSL to /data/local/tmp
20/019/2012 16:19:40 - INFO - Pushing C:\Program Files\Flashtools 0.8.6\Flashtool\custom\features\UnlockBL\files\qsd8250\mapper_2.6.29-00054-g5f01537.ko to /data/local/tmp
20/019/2012 16:19:40 - INFO - Pushing C:\Program Files\Flashtools 0.8.6\Flashtool\custom\features\UnlockBL\files\qsd8250\fixPart to /data/local/tmp
20/019/2012 16:19:40 - INFO - Running runfixPart as root thru sysrun
20/019/2012 16:19:41 - INFO - Successfully applied fixPart. Rebooting
20/019/2012 16:19:41 - INFO - Waiting for device
20/019/2012 16:19:42 - INFO - Device disconnected
20/019/2012 16:19:53 - INFO - Device connected with USB debugging off
20/019/2012 16:19:53 - INFO - For 2011 devices line, be sure you are not in MTP mode
20/019/2012 16:19:57 - INFO - Device connected with USB debugging on
20/020/2012 16:20:10 - INFO - Running runbootwrite as root thru sysrun
20/020/2012 16:20:11 - INFO - Successfully applied unlock. Rebooting
20/020/2012 16:20:11 - INFO - Running runClean as root thru sysrun
20/020/2012 16:20:13 - INFO - Device disconnected
20/020/2012 16:20:24 - INFO - Device connected with USB debugging off
20/020/2012 16:20:24 - INFO - For 2011 devices line, be sure you are not in MTP mode
20/020/2012 16:20:33 - INFO - Device disconnected
20/020/2012 16:20:36 - INFO - Device connected with USB debugging on
20/020/2012 16:20:36 - INFO - Connected device : X10
20/020/2012 16:20:36 - INFO - Installed version of busybox : BusyBox v1.19.0 (2011-08-14 23:46:58 CDT) multi-call binary.
20/020/2012 16:20:36 - INFO - Android version : 2.3.3 / kernel version : 2.6.29-00054-g5f01537
20/020/2012 16:20:48 - INFO - Root Access Allowed
20/023/2012 16:23:12 - INFO - Device disconnected
20/024/2012 16:24:10 - INFO - Log written to C:\Program Files\Flashtools 0.8.6\Flashtool\flashtool_2012-12-19_04-10-47.log
Don't 'freak out' when you see "Bootloader status : UNROOTABLE" scroll across the screen. My heart sunk when I saw that, but I let the first phase of the process complete and then connect the phone to the USB cable after the phone had re-booted with Flashtool 0.8.6 (in my case) still running and the process completed. In my case I got my phone back unlocked and still rooted. All good.
I'm pretty sure my bootloader was not locked when I started out a year or so ago, but I can't be absolutely sure; so somehow it's seems to have become locked during that time. Maybe because I was just recovering the same build each time I never installed anything else to check.
Like the OP, I originally rooted my phone by using 0.2.9.1 GB-ready using a convoluted process compared to todays one click root process.
Now when I flash a ftf file in Flashtool it runs through without any errors.
I was then able to go on and install [CM10] v4 (Torch) by: scritch007 without any problems.
Hope some of this information can help others.

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My downloaded Flashtool has a virus. So I use the 0.9.0.0 version and it works ok.

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I had the same issue too with v 0.9.9.0. for rooting I use v 0.6.8.0