Once numbers and/or lag starts getting high, how units handle orders starts becoming weird.
Also, based on other threads I have seen, there seems to be a lurking "AI ships get stuck" bug somewhere with threat, threat fleet, and possibly special forces. Wouldn't surprise me if a similar issue existed with minor faction logic.
To both chemical_art and Spikey00:
Do the "zombies" respond eventually? If so, it could just be the sheer number of units means the engine has to wait several seconds between the order being given and the unit taking action.
If not, do the "zombies" finally do stuff once numbers start getting pruned to more reasonable levels? Although that would point to "unit order scheduler" having a major "starvation" issue (something to be addressed), it would at least explain that it was a "too much to do in a single game cycle" type phenomenon.
If not, do they "wake up" upon a save/load cycle?
If so, that may point to that bug mentioned in the other threads (similar issues with AI ships "stop trying to attack when they should" that get fixed upon a save/load cycle)
If they still don't "wake up" after that, then you may have encountered a new, different bug (like unit orders getting "lost" in high lag or high stress situations).