ok maybe best to wait till version 6, however some of what you are experiencing was covered in a recent post and this mod:
TheDarkWraith_DC_Water_Disturbance_v4_0_SH3
was determined to possibly be related to the CTD after sinking a ship. Check out this post if your interested:
http://www.subsim.com/radioroom/showthread.php?t=203350
toward the end you can see some possible causes, in my case it was defitely Lifeboats and debris 4 conflicting with another mod i have
