This may sound like an old problem but believe me, it's not. Let me explain.
I've rooted my Transformer TF101G (B90) last year sometime on 3.2.1. This works fine with no issues. I've flashed ClockworkMod after installing ROM Manager. This worked fine, I can boot normally, I can boot to recovery, no problem.
With the latest update available from ASUS via the web, I decided to to allow the annoying icon complaining about upgrading to download and run the upgrade. After downloading the update the Pad rebooted so if to install the new update. This landed me on the CWM with an error message that stated the verification (or something failed). After this, the Transformer wouldn't boot directly to Android, but ended up booting to the recovery partition every time. I had to use the fastboot option to "cold boot" into Android.
This was annoying, so I googled and found the solution on this forum to fix the issue with 188.8.131.52 that kept rebooting to recovery. This solved that problem and I was still able to boot to recovery whenever required.
I decided to update CWM to version 184.108.40.206 via ROM Manager. This seemed to work via ROM Manager, but restarting the transformer and going to recovery showed version 220.127.116.11 still. So I went back to ROM Manager and it showed that it was upgraded to 18.104.22.168. I decided to update this to ClockworkMod Touch by purchasing it via Google market to support the guys that do development on it. This claimed to install also. "Reboot into Recovery" from ROM Manager still showed version 22.214.171.124.
I was now very confused.
So I decided to downgrade CWM from the 126.96.36.199 version it stated was installed to version 188.8.131.52. This worked according to ROM Manager, but rebooting into recovery still showed 184.108.40.206. I mean, WTF!
In the meanwhile the freeken update icon on the task tray still complained about updating Android. I allowed it again to try and update. At the point it rebooted it left me stuck on the "EEE Pad" screen.
Booting up with Vol - and Power takes me to the screen that gives you an option to press Vol + to boot to RCK. Doing so the Pad freezes at "Booting Recovery Kernel Image". My PC then detects USB ADB interface but any adb commands respond with "error: device offline" or "error: device not found".
Booting up with Vol + and Power leaves the screen blank. My PC then detects an USB APX interface. Using "fastboot -i 0x0b05 flash recovery recovery-clockwork-touch-220.127.116.11-tf101.img" only responds with "waiting for device".
The only way to boot my tablet at the moment is to use the "cold boot" option.
I would like to think I've tried everything out there and would appreciated anybody that could point me to maybe something else I could try.
PS: In ROM Manager I get "An error occurred while attempting to run privileged commands" when I use the "Fix Permissions" option.