Ive been keeping my eye on this on ubi and subsim, and i believe this is a "stock" issue with version 1.5.
edit:
For example, this post was made
http://forums.ubi.com/eve/forums/a/t...5/m/8721047836
2 days ago. TMO came out last night, so its a safe bet its a stock issue.
edit:
I have to wonder, if anyone whos run into this bug, has been loading a game that was saved while submerged? Maybe a workaround is to always save while surfaced? Just guessing.