Do you use any mods/fixes/patches? It's possible that a sort of incompatibility problem between them causes the diesel bug.
Is your WO on the bridge when you're on the surface? Perhaps the waves are such big that the game thinks you're submerged therefore cannot run on diesels. Haven't you set wave height double in SH3Cmdr by chance?
Have you tried loading an earlier save?
If nothing helps, you'll have not too many choices left. Leave this career and start a new one far far away from those cruel North Atlantic waters.
Hope could help a little.