Check if there is a fleet jumping back and forth between the same two systems. NPRs frequently get themselves "trapped" in this way when an order to, say, refuel at the nearest colony causes them to jump into a hostile fleet (alternatively it may have something to do with the system danger rating, I'm really not sure), and since NPRs can instantly re-jump they flee through the jump point, and then repeat the process over and over while trying to fulfill their orders.
Usually the problem can be solved by relocating the fleet involved so that they cannot immediately jump again.
Any idea how to find fleets that are doing that? I can't see any such fleet in-game, and I'm not sure what to look for in the database.
EDIT: From looking in the ship table it seems there are no ships experiencing any jump shock. I know jump shock wears off more quickly for the NPRs, maybe it's wearing off within the 60 seconds?
Check FCT_GameLog for NPR fleets reporting jumps back and forth or an inability to complete orders.
Hmm, I'm getting a repeated event "Destination of
Large Hive Fleet 001 cannot be found. Please issue new orders." But it's not coming in 60 second increments, only showing up every couple of minutes. Also, every time I've checked it hasn't had any orders listed in the movement orders table. However, apparently there's also currently
boarding combat between two different Swarms! so maybe once that finishes the slowdown will clear up.
Thanks for recommending I check FCT_GameLog -- for some reason I completely missed it.