I've experienced similar problem too on my custom maps. I think I've figured out the pattern.
If I load up the map from the console and save the game, and I reload the game later, I almost always get the AI_Disabled message. But if I load up the map from the console each time (instead of loading them from a previously saved game), I almost never get this message. Occasionally, I'll get this problem over and over, but it'll resolve when I restart HL2.
I figure it's a path bug from Valve. I hope they're going to fix it soon. Because sometimes even after I enabled the AI, the info_node information still seem to be missing (because the Combines don't seem to know where to go).