I found the cause of bugs as described in previous post, and was able to fix them. The systems not being recongized was from me forgetting to use the star system's X,Y coordinates. So basically whoever controls the top left part of the galaxy (the first 4 grid cells on top left) can migrate to any star system. It's fixed
Here's the latest version (read previous blog posts about how to correctly set up the game): Beyond Beyaan - April 16 2011
Again, please let me know of any bugs or improvements I can do!