Thank you all!
EDIT for correction: its actually a hard coded crash dive bug. See this thread for detailed infomation if you are having similar problems:
http://www.subsim.com/radioroom/showthread.php?t=92883
In short: dont abort crash dives. Let the boat dive to its crash dive depth and level off before you do any depth changes
if you did an emergency ALARM - or you are bugged. :p