Pesty,
Your Hydran ally/enemy problems might have to do with the map set up. Last week, before you reset, I took a neutral planet that had 100 Econ and 50 DV. The only mission it would offer me was Homeworld Assault and I always got the H-PHY planet and Hydran opponents. As soon as I took the hex, my enemies turned to Mirak. If the server is somehow interpreting that Neutral planet as the Hydran Homeworld it might explain why the Hydrans don't show up on a planet to start and why they seem to be allied and opposed to some races at the same time. Of course, the ISC showed up on a 10/10 planet, not a Homeworld, so I may be way off here.