OK, I think the problem is in AI_construction_vehicles.txt file. In contrast to "normal" AI, neutrals have "colonizer" entry only in explore and not connected states. If for some reason AI in any other state, it won't build colony ships. Here is my quick fix:
1046742418.txt
Replace neutral001_AI_construction_vehicles.txt with this new file. (proportions/pictures/raceneutrals/neutral001 folder. If it fixes the problem, other neutrals should have this file too !!