1. This happens when you change the relations of the AIs before the game. If set them to anything other than "unknown" you will be able to talk to them before discovering them, if you have the requisite technology.
2. Trading values have always been a bit screwy.
3. You wont have to re-install. Just set relations back to unknown.
4. They need the Orbital Fleet Manager to defend as a fleet when orbiting a planet.
Sentient species taste better...