[Sony Xperia S, Acro S, Ion] Toledo_JAB:
hope it helps

ok so lets go through it....

#the start tells that flashtool(FT) started ok and is version 9.8 (newest that i know of) and that no device is connected#

15/037/2012 20:37:59 - INFO - <- This level is successfully initialized

15/037/2012 20:37:59 - INFO - Flashtool Version 0.9.8.0 built on 2012-10-01 19:35:32

15/037/2012 20:37:59 - INFO - You can drag and drop ftf files here to start flashing them

15/038/2012 20:38:04 - INFO - Device disconnected

#this part you started a flash session for this firmware, connected phone in flash mode, it #started to flash and failed immediately. note the error entry flash aborted. it looks like it never even #started. as it should have said flashing header after checking.#

15/040/2012 20:40:01 - INFO - Selected LT28i_4.0.4, 6.1.E.1.19_Rogers (Canada).ftf

15/040/2012 20:40:01 - INFO - Preparing files for flashing

15/040/2012 20:40:04 - INFO - Please connect your device into flashmode.

15/040/2012 20:40:17 - INFO - Opening device for R/W

15/040/2012 20:40:17 - INFO - Device connected in flash mode

15/040/2012 20:40:18 - INFO - Start Flashing

15/040/2012 20:40:18 - INFO - Processing loader

15/040/2012 20:40:18 - INFO - Checking header

15/040/2012 20:40:18 - INFO - Ending flash session

15/040/2012 20:40:18 - ERROR -

15/040/2012 20:40:18 - ERROR - Error flashing. Aborted

#then looks like you left phone plugged in on flashmode#

15/040/2012 20:40:18 - INFO - Device connected in flash mode

15/040/2012 20:40:31 - INFO - Device disconnected

#this section with the regular timing looks like minor bootloop or you were unplugging/replugging the phone quickly while not in flash mode#

15/040/2012 20:40:37 - INFO - Device connected with USB debugging off

15/040/2012 20:40:37 - INFO - For 2011 devices line, be sure you are not in MTP mode

15/040/2012 20:40:43 - INFO - Device disconnected

15/040/2012 20:40:52 - INFO - Device connected with USB debugging off

15/040/2012 20:40:52 - INFO - For 2011 devices line, be sure you are not in MTP mode

15/041/2012 20:41:01 - INFO - Device disconnected

15/041/2012 20:41:11 - INFO - Device connected with USB debugging off

15/041/2012 20:41:11 - INFO - For 2011 devices line, be sure you are not in MTP mode

15/041/2012 20:41:19 - INFO - Device disconnected

15/041/2012 20:41:28 - INFO - Device connected with USB debugging off

15/041/2012 20:41:28 - INFO - For 2011 devices line, be sure you are not in MTP mode

#here some thing changed. the phone booted with debug enabled and disconnected (maybe part of previous bootloop still since the phone did NOT fully boot)#

15/041/2012 20:41:32 - INFO - Device connected with USB debugging on

15/041/2012 20:41:37 - INFO - Device disconnected

#now the phone almost boots but looks like locked up, notice how all times are 41:37. then you either unplugged or phone rebooted#

15/041/2012 20:41:37 - INFO - Connected device : LT28

15/041/2012 20:41:37 - INFO - Installed version of busybox : N/A

15/041/2012 20:41:37 - INFO - Android version : 4.0.4 / kernel version : / Build number : 6.1.E.1.19

15/041/2012 20:41:37 - INFO - Phone in recovery mode

15/041/2012 20:41:37 - INFO - Root Access Allowed

#here it appears that the phone has full booted and FT connects to it correctly and pushes the FT tools to the phone (this normally happens on first connection to FT after a good flash)#

15/041/2012 20:41:48 - INFO - Device connected with USB debugging on

15/041/2012 20:41:48 - INFO - Connected device : LT28

15/041/2012 20:41:48 - INFO - Installed version of busybox : BusyBox v1.19.0 (2011-08-14 23:46:58 CDT) multi-call binary.

15/041/2012 20:41:48 - INFO - Android version : 4.0.4 / kernel version : 3.0.8+1.0.21100-30145-01962-g90d4b42 / Build number : 6.1.E.1.19

15/041/2012 20:41:48 - INFO - Installing toolbox to device...

15/041/2012 20:41:48 - INFO - Pushing C:\Flashtool\custom\root\ftkit.tar to /data/local/tmp

15/041/2012 20:41:49 - INFO - Running installftkit as root thru sysrun

15/041/2012 20:41:50 - INFO - Root Access Allowed

15/041/2012 20:41:57 - INFO - Device disconnected

#this looks like the bootloop you speak of if it just keeps happening over & over, on the phone you may have seen the XPERIA bootsplash then reboots#

15/042/2012 20:42:08 - INFO - Device connected with USB debugging on

15/042/2012 20:42:08 - INFO - Connected device : LT28

15/042/2012 20:42:08 - INFO - Installed version of busybox : BusyBox v1.19.0 (2011-08-14 23:46:58 CDT) multi-call binary.

15/042/2012 20:42:08 - INFO - Android version : 4.0.4 / kernel version : 3.0.8+1.0.21100-30145-01962-g90d4b42 / Build number : 6.1.E.1.19

15/042/2012 20:42:08 - INFO - Root Access Allowed

15/042/2012 20:42:16 - INFO - Device disconnected

i have had times when i had to flash 3-4 times before it would take. i would definitely re-download the stock firmware as it appears maybe corrupt. did you modify the file your flashing? do you have CWM? if so enter and format system & cache(should end bootloop but will leave no ROM so re-install a back-up). if not next time you get it to flash mode flash the stock firmware with wipe system & cache at least. i recommend a full wipe (check all). if your going to mess with system files i would use CWM and make a working back-up, better safe than this ;)