I can't remember off the top of my head if this applies to automatic abilities in general, but I do know it seems to effect the repair structures.
I just started playing a new level and had a pirate invasion on one of my home planets
The only defences I had were a couple of missile platforms, a repair platform and 3 capital ships
I noticed that the repair station didn't automatically start repairing the damaged ships or missile platforms right away after it'd completed the previous repair, infact it seemed to take several seconds to kick off again, despite the fact it had plenty of antimatter and the cooldown had expired.
It wasn't due to the fact there wasn't anything in range, or that the items in range weren't damaged enough, it just didn't seem to kick in fast enough.
Anyone else experience this?