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I've had this issue as well. Are you playing fall of the jedi? I have found that if you play just the clone wars the problem doesn't occur.
There's nothing you can do I've gone directly to their problem forums and they told me it's a known issue. So all you can do is wait for the 1.2 patch
How do you Mod folder it? (I have the gold edition) I created a folder called mods but I'm sure there's more to it then that. How do you start the game
Great mod works fine mostly. But now after playing GC for a long time I suddenly can't select space units. Also some units in the galaxy view I can't get to move. Anyone else having this problem? If so how do I fix it? I haven't made any of my own changes to game other then adding some higher quality music but that shouldn't trigger anything.