Whoops never mind, turns out the reason is I forgot to set up one of the items in the interrupt condition. So my requests would finish, the interrupt would clear, but the same interrupt would instantly trigger over and over in an infinite cycle that was so rapid I guess I couldn't even tell it was ...

I'm setting up some interrupts for my Aquilo ship so it will automatically go pick up materials on other planets needed for the components there when they run dry. I don't want to spending time doing a solar system tour when 9 times out of 10 all I really need to do is drop some science packs back ...