FYI, I had this exact same problem and I'm not even rooted, so it may not be due to your new kernel. Either hard reset or re-dock fixed it. I can't remember which.
What a bunch of crap...I used to like Engadget...
Engadget - Eee Pad Transformer gets overclocked to 1.4GHz, deemed less than stable http://engt.co/jur5AW
Netarchy, is the kernel for the Transformer based on Google's 2.6.35?
EDIT: NVM, filing through your github now I think you could very easily get it up to 1.5GHz. Take a look at the modifications I did on the Xoom (https://github.com/coolbho3k/Xoom-OC....36-honeycomb/); did you adjust the power regulators for the increased voltage at 1.4? I think 1250 mV is stable at 1.5 for most people on the Xoom.
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