Long version: There is a bug in Empire at War called the selection freeze bug, where after a certain number of objects have existed in the game, the game will stop being able to track them. It's an engine thing, so it's not directly fixable. Having a lot of planets and a lot of factions moving makes this bug occur incredibly quickly, as not only is the game keeping track of player vs AI conflicts, the AI factions through a ton of shit at each other and go back and forth. This meant that the game was essentially unfinishable with 100 planets and 4+ active factions. To counteract that, we made it so in Art of War in 2.1, only three factions had active galactic AI, typically either the PA or EotH was disabled (we allowed more on smaller maps). However, since then Pox and Fregge made the Defreezer too, which allows you to reset the problematic counter and continue as normal, so we released a patch re-enabling it.
Short version: Download the patch to re-activate AI:
http://thrawnsrevenge.com/forums/index.php?topic=4976.0