That's a weird one!
Hmm. So if the problem persists across restarts of the game, this sounds like it's an issue with the operating system, possibly triggered by something the game does, but ultimately probably not
due to something the game does, if that makes sense. The game doesn't carry any state - aside from some config settings - across application restarts, and any problem like (say) an in-game memory leak should be completely cleared by a restart, so it's not that.
Btw, do you have to load into the same campaign save for the problem to show up, or does it show up regardless of that? It sounds like the latter, but it'd be good to confirm.
As to what the issue might be, it's really hard to say. Lag like that on a system could mean, say, lots of pagefile swapping. You might (at your own risk
try
disabling that, to see if it helps. Another possibility is a graphics driver issue.
Another, more distressing possibility, is a hardware issue. For example, if something Starsector does follows a pathway in the video card that's "bad", that could accumulate across game restarts, but be cleared by a PC restart. Or it could be something that an OS reinstall would fix (though I'd hardly recommend trying that just to see).
It really is just very hard to say exactly what the problem is. Something bad accumulates across restarts, right. If the system is working properly, that seems impossible. But narrowing down what the issue might be beyond that is ... non-trivial. Like, you probably don't have a spare video card laying around to see if swapping that in might help or not.