What about the design of your defense units? Do the satellites or the fighters have stealth? I've seen a bug where a stack of units at a warp point is automatically assumed to be cloaked when an enemy unit comes through just because ONE of the units has the cloak ability. It was quite annoying to put 100+ satellites on a warp point and have battleships sail right by them & go for the colonies in the system... I thought it had been fixed, but maybe not. I've gotten in the habit of not putting units with cloak ability on warp points.
You might want to play with 'autosave' turned on so that if you see this again you can send the save games to MM.
[ 19 March 2002: Message edited by: Baron Munchausen ]