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What keyboard have you been using?
I've never had issue with SmartKeyboard. Maybe only on Chrome... but then again Chrome has never played nicely with me.
Same, only issues with Chrome using stock or swiftkey keyboard
My situation exactly. With Chrome using Swiftkey, the keyboard would disappear. So I just quit using Chrome. I have never had any good luck with it anyway on my phone.

Have you tried the Chrome beta? I've had a lot more success with it than the standard release. Not nearly as many graphical glitches and no (that i've seen so far) disappearing keyboard issue.

Ive just been using the keyboard that came on the ROMs. Ive been using Harmonia, MidnightRom Senseless, and now MidnightRom Jellybean. Sometimes the keyboard would disappear while texting but I dont think thats happened since I switched to MidnightRom J. Ill give the chrome beta a try.
Edit: The chrome beta crashes every time I open it, guess I wont be using that.