Two common sources of really long 5 second intervals are:
1. NPRs chasing each other through a stabilized jump point. This will NEVER end, because ships can standard transit with no delay. What happens is a ship sees a threat, so it runs away through the jump point. So the other ships follow. So it runs back. They follow. At no point will they be able to fire (you have to wait on one side of the jump point with targets set, so that when they come BACK you shoot them). Transits require no fuel and NPRs do not use maintenance. This will continue indefinitely.
2. Orbital bombardment. It's wildly inaccurate so if an NPR decides to try to help its ground forces in this fashion, it may be stuck doing so for a very, very long time.
A good habit to get into is to place passive sensor buoys on every jump point (even in NPR territory...they won't mind). This allows you to notice both of these options. You can then do something about them. I've created a Spacemaster race with max tech, and I teleport super battlestations around to blow up the fleeing ship in case 1 or to provide additional fire support in case 2.
You can also open the database using DB Browser for SQLite. Look at the last rows of the FCT_GameLog table. That will help you figure out what is happening, at least. Spacemaster can't see the NPR's event logs, but the database DOES contain them.
