This has happened three times now and is rather odd. Playing as Humans with the Altarians, Korx, Drengi, and Arcerans. The 2nd or 3rd race I initially encounter immediately states that a state of war exists between us and while some quick trading will usually bring a peace treaty, it doesn't always work. Took over two years to reach a peace treaty on one occasion.
The next issue regards the purple suns that usually have a high PQ planet as part of its solar system. In every game to date the purple solar system does not have a high PQ planet when it is within 5 squares of my homeworld, yet all of the other purple solar systems still have a high PQ planet when they are beyond 5 squares from my homeworld.
Final glitch consists of custom ships that disappear after about two years...the ships are still available and exploring, attacking, defending etc. but they are no longer veiwable on the main screen. Oddly enough this also seems to cause a black hole glitch, in that if an invisible custom ship path goes through a black hole it jumps just like it was a survey ship. The black hole also travels with the ship and reappears where the ship does. It does not follow the ship any more but is rather interesting when it drops your small fighter into enemy space and you have not explored that area.
These all happened post release and a clean download. All of my games have been played on an immense map with everything set to random except number of habitable planets which is set to common. All events are on except Assencion Victory. Number of races is 4 with all having random intellegence.
Sorry no screen shots available but this is a carry over from pre-release reports I made.