I've been playing SH3 pretty constantly for just over a year (LSH-2015 at the moment) and never had this problem:
The sun is coming up at around 02:00 and setting around 14:00.

It's August 1940 and I'm in the western Mediterranean, though it actually started just before I went through Gibraltar.
I've done a bit of searching and can't find much about it or many people reporting any similar problems. I only ever use up to x32 TC (usually no higher than x8) and it seems to have started after loading up the save a couple of days ago. The only thing I can think of is I've possibly messed up the save file somehow which is actually a first for me!
Anybody else had anything similar happen or know of any potential solutions?