To add to what Pisces describes, it also might be a mod soup situation of the not-very-nice variety. Any shelling out to Windows and returning to an active game can cause similar issues. But around ports in some mods can be very busy and bring the computer to a crawl, depending upon your hardware.
Also, certain mods have what I call "run-a-way" spawns accidentally built into them. What happens is that a ship gets added to a mod, and set to face a certain direction, but the modder neglected to set the "speed" to zero, and did not "dock" the ship. Therefore, when it comes time to spawn, it departs at the "default" speed of 5 knots. Since it is only in the database until you get within its actually 3D spawn range, it will "circle" the globe on that particular heading. The next time a spawn for that particular "group" comes along, it adds another. Lather rinse repeat, and the next thing you know, you have a 30+ DD "Task Force" that will take your computer down and CTD you hard, even at 1x TC. If you ever experience that, post about it with your mod list, and we'll try to fix you up. I had a fix for FOTRS v1.3 around here somewhere... if I could ever find anything in this mess... I also used to have a 010 Editor script that could find them all, but I never got it set-up to do a quick-fix for me... [rummages through hard drive files and empty space]
