O kernel é em modo flashmode não é?
Device connected with USB debugging on
13/024/2012 18:24:02 - INFO - Connected device : ST25
13/024/2012 18:24:02 - INFO - Installed version of busybox : N/A
13/024/2012 18:24:02 - INFO - Android version : 4.0.4 / kernel version : 3.0.8+ / Build number : 6.1.1.B.1.54
13/025/2012 18:25:10 - INFO - Selected Xperia U_ICS 4.0.4 kernel_nu.ftf
13/025/2012 18:25:10 - INFO - Preparing files for flashing
13/025/2012 18:25:10 - INFO - Please connect your device into flashmode.
13/025/2012 18:25:17 - INFO - Device disconnected
13/025/2012 18:25:41 - INFO - Device connected in flash mode
13/025/2012 18:25:41 - INFO - Opening device for R/W
13/025/2012 18:25:41 - INFO - Reading device information
13/025/2012 18:25:41 - INFO - Phone ready for flashmode operations.
13/025/2012 18:25:42 - INFO - Start Flashing
13/025/2012 18:25:42 - INFO - Processing loader
13/025/2012 18:25:42 - INFO - Checking header
13/025/2012 18:25:42 - INFO - Flashing data
13/025/2012 18:25:43 - INFO - Loader : S1_Root_3065 - Version : R5E006 / Bootloader status : NOT_ROOTABLE
13/025/2012 18:25:43 - INFO - Processing kernel.sin
13/025/2012 18:25:43 - INFO - Checking header
13/025/2012 18:25:43 - INFO - Flashing data
13/025/2012 18:25:44 - INFO - Ending flash session
13/025/2012 18:25:44 - INFO - Flashing finished.
13/025/2012 18:25:44 - INFO - Please unplug and start your phone
13/025/2012 18:25:44 - INFO - For flashtool, Unknown Sources and Debugging must be checked in phone settings
13/025/2012 18:25:44 - INFO - Device connected in flash mode
É mesmo isso que tem de aparecer

Depois ligas esperas um pouco reinicias e fazes o
Root... depois flash o outro Kernel e prontos