That makes sense then. Your troops can't stay on his planets if you sign a peace treaty with him. The game engine has no idea when a troop transport of yours will be around to pick them up (as the transport could easily have left, or been blown up by other enemy ships). So, it just gives them to the defender.
I guess it's a good enough decission on the computer's part... sure beats the whole game crashing!
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Jimbob
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