Also, I got a cryptic message: Sub-pulse adjusted due to potential fleet interception. The sub-pulse thing I understand. The potential fleet interception I do not. What does that mean?
It depends on the context. Were you looking around in SM mode when you got this?
It might imply that you're about to be visited by an NPR.
(I don't know for sure, that particular message might only appear in SM anyway.)
Essentially, fleets are close to detection range of each other. They might be yours, or they might be an NPR half way accross the universe.
If your longer time increments suddenly stop passing completely without obvious interruptions, it's an NPR battle.
They need to play by the same rules we do. I'd suggest checking the Automatic Turns box, hitting an increment of a day or so, and letting it grind for a few
minutes.
If, on the other hand, the problem is something on your end, you'll probably know.
By the way, Steve wrote up a tutorial about this somewhere around here. I suggest reading it if you can find it, the question you ask is fairly common.
Check the Useful Links topic here.
Hope this helps,
Zack.