Could you give us this error exactly? If you can boot and you have root, you SHOULD be able to upgrade, it just may require some manual work...
when i like install with recovery:
"E

rohibit update as a result of checking version or base sku"
when i like install whit ota
"the system is update" something like that, my language is in spanish
You have used flasher to get to where you are now? R6B?? If so then your region has change and you will need the US for wifi only or the Poland (i think) for +3G. Try to install any zip from recovery and use adb pull /tmp/recovery.log and post it here. We will tell you what is happening.
yes, i used flasher to get r6b prerooted.
my tablet is US version, the log is:
Starting recovery on Sun May 12 21:58:07 2013
can't open /dev/tty0: No such file or directory
framebuffer: fd 3 (1280 x 800)
recovery filesystem table
=========================
0 /tmp ramdisk (null) (null) 0
1 /hwconfigs ext2 /dev/block/mmcblk0p1 (null) 0
2 /configs ext4 /dev/block/mmcblk0p2 (null) 0
3 /system0 ext4 /dev/block/mmcblk0p3 (null) 0
4 /system1 ext4 /dev/block/mmcblk0p4 (null) 0
5 /cache ext4 /dev/block/mmcblk0p5 (null) 0
6 /misc emmc /dev/block/mmcblk0p6 (null) 0
7 /staging ext4 /dev/block/mmcblk0p7 (null) 0
8 /blflags ext4 /dev/block/mmcblk0p8 (null) 0
9 /datapp ext4 /dev/block/mmcblk0p9 (null) 0
10 /log ext4 /dev/block/mmcblk0p10 (null) 0
11 /data ext4 /dev/block/mmcblk0p11 (null) -32768
12 /sdcard vfat /dev/block/mmcblk1p1 /dev/block/mmcblk1 0
13 /boot emmc boot (null) 0
14 /recovery emmc recovery (null) 0
15 /system ext4 system (null) 0
16 /vendor0 ext4 vendor0.img (null) 0
17 /vendor1 ext4 vendor1.img (null) 0
Command: "/sbin/recovery"
ro.secure=1
ro.allow.mock.location=0
ro.debuggable=0
persist.sys.usb.config=mtp
ro.build.id=TID0142
ro.build.display.id=TID0142
ro.build.version.incremental=121116001
ro.build.version.sdk=15
ro.build.version.codename=REL
ro.build.version.release=4.0.3
ro.build.date=Fri Nov 16 01:16:55 JST 2012
ro.build.date.utc=1352996215
ro.build.type=user
ro.build.user=integ-build
ro.build.host=build8
ro.build.tags=test-keys
ro.product.model=SGPT12
ro.product.brand=Sony
ro.product.name=SYS_052
ro.product.device=txs03
ro.product.board=txs03
ro.product.cpu.abi=armeabi-v7a
ro.product.cpu.abi2=armeabi
ro.product.manufacturer=Sony
ro.product.locale.language=en
ro.product.locale.region=US
ro.wifi.channels=
ro.board.platform=tegra
ro.build.product=txs03
ro.build.description=SYS_052-user 4.0.3 TID0142 121116001 test-keys
ro.build.fingerprint=Sony/SYS_052/txs03:4.0.3/TID0142/121116001:user/test-keys
ro.build.characteristics=tablet
ro.opengles.version=131072
wifi.interface=wlan0
wifi.wpa_supp_ready=0
persist.tegra.nvmmlite=1
windowsmgr.max_events_per_sec=135
ro.tether.denied=true
ro.sony.sound.enabled=true
ro.sony.display.release=release6b
ro.product-res-path=vendor/framework/SemcGenericUxpRes.apk
ro.sony.autovolume.threshold=10
ro.sony.update.server=info.update.sony.net
ro.sony.update.category_id=ST001
ro.config.alarm_alert=Alarm.ogg
ro.config.notification_sound=Notification.ogg
ro.config.ringtone=Ringtone_XPERIA.ogg
drm.service.enabled=true
dalvik.vm.heapstartsize=5m
dalvik.vm.heapgrowthlimit=48m
dalvik.vm.heapsize=256m
ro.sony.wifisleep=0
ro.semc.enhance.supported=true
ro.semc.clearaudio.supported=true
ro.somc.dmnorm.supported=true
ro.setupwizard.mode=DISABLED
ro.com.google.gmsversion=4.0_r6
ro.com.google.clientidbase=android-sony
dalvik.vm.dexopt-flags=m=y
net.bt.name=Android
net.change=net.bt.name
dalvik.vm.stack-trace-file=/data/anr/traces.txt
tf.enable=y
ro.sony.wan.ipv6.enable=false
persist.sys.sony.cabc.disable=0
persist.sys.sony.hdmi.disable=0
ro.sony.dlna_dms.enabled=false
ro.somc.social_product_model=PRODUCT_MODEL_TABLET
ro.sony.irremote.protocol_type=2
ro.sony.ols.eula=1
ro.pss.ps1content_disable=1
ro.factorytest=0
ro.bootmode=unknown
ro.baseband=unknown
ro.carrier=unknown
ro.bootloader=0x00000006
ro.hardware=txs03
ro.revision=0
init.svc.recovery=running
init.svc.nfx_daemon=running
init.svc.radbd=running
-- Install /sdcard ...
Finding update package...
I:Update location: /sdcard/update.zip.zip
Desklunvr update package...
Opening update package...
I:1 key(s) loaded from /res/keys
Verifying update package...
I:comment is 1465 bytes; signature 1447 bytes from end
I:whole-file signature verified against key 0
I:verify_file returned 0
Checking version is passed, 111104048 -> 121116004
Fail to open /configs/region.zip
E

rohibit update as a result of checking version or base sku
Installation aborted.
Edit:
I used this files
US & Canada
Jelly Bean
info.update.sony.net/ST002/txs03_201/contents/0006/signed-txs03_201-ota-130329006.zip
ICS Release 6b
info.update.sony.net/ST002/txs03_201/contents/0005/signed-txs03_201-ota-121116004.zip