So far I've only seen this problem with Skipjack, Permit, Sturgeon, 688(i), and the Ohio. I haven't tried any of the Russian boats to see if it happens with them.
EDIT: Well I tried the Russian boats and couldn't get it to replicate. Tried Nautilus and couldn't get it to do it again with it. But the problem seems to be gone now after I disabled and re-enabled all activated mods. Seems to have been a small case of mod soup and that sorted it out. Back to work I go.