That's passed now. May or may not have been related to alien ships prowling my civilian shipping lines and having civvie ships appear and disappear from their sensor screens.
However, a few years later I encountered another problem (now on 5.02). I had defended the jump point the alien vessels were using to enter my system and raid my civilian ships for about 5 years. I managed to destroy a handful of enemy units as they jumped in. However, my frigates eventually had to return to resupply at Earth, and not a month later, another alien ship appeared in the system. Fortunately, a level 10 listening post on an asteroid picked them up about two billion kilometres away from the main trade route.
I immediately dispatched three missile frigates and a SWACS vessel to intercept the 19,200-ton target. However, shortly after it was detected by the LP, interrupts became stuck at 60 seconds. According to SM Only event messages, the reason is: "Increment length adjusted as a ship is within firing range". That has to be some freak coincidence with some other thing happening elsewhere in the galaxy, as none of my weapons have a range of 2 billion km. It's highly unlikely the enemy target has that kind of range, either, as their tech was considerably behind mine. I had seen that class before, and it has nuclear pulse engines, duranium armour, poor sensors, etc.
Any ideas? These 60-second skips have been going on for over 2 game hours.