Take a look at this thread:
http://www.subsim.com/radioroom/showthread.php?t=132471
Near the bottom of that thread you'll notice I did the same thing as you. Tho I didn't mention it there, I also crashed-dived (just to get under quicker), saved the game, reloaded, blew ballast (to surface quicker), and no more CO
2 issues...
I have not been able to reliably reproduce the bug, which makes it harder to find a consistent way to fix it.