So I finished my patrol last night. The smoke followed me throughout, all the way back to Freemantle. When I went out on the new patrol (after being in the base) the smoke was gone.
I was thinking about what was different about that particular patrol that may have triggered the problem. :hmm: As I described above, I initially thought that it might be the hidden "static" damage, but that doesn't appear to be the case. The only other thing I could think of that was different was that I sank a fishing boat, and a junk with the deck gun. I usually don't bother with them, but I'd went out of my way to investigate a radar contact, and the seas were calm so I took a little target practice.
Unfortunately, I don't have a save from before I sank those two boats, so I can't easily check this. On my current patrol I'm keeping an eye out for similar craft, but of course now that I actually want to find some I can't.
I'll post again if I find anything interesting.