I've got excactly the same issue. At first i thought it were some maps that didnt work properly. After testing with only me and 1 enemy AI, all maps worked.
Tried reinstalling, both the game and the mod. Games are properly patched too.
Also had the sweet FX installed first time, uninstalled it to check if it would do anything. The issue remains.
-Edit-
LOL
As i was writing this post i got the idea to test if vanilla worked with multiple AI's. Never tested it because i was interested in the mod and i already knew Expansion. Worked fine.
After that i switched back to Edain's mod and all the sudden it worked. Got Multiple AI's in teams but no clue what fixed it. Also tried setting factions for them all too see if 1 was a issue and also tried not giving them places and teams and vice versa. Nonetheless it all worked perfectly fine.
Really seems that starting a map without the mod fixed the issue.
Hope it works for you too.
Grapjas