Actually, the AI breaks rules regarding targeting. Just because you can't target them, doesn't mean they can't target you. In fact, if you were to make a ship with a plug-in that couldn't be targeted, and then pit it against another AI ship, that AI ship would still be able to target it and fire turrets on it. I know, it sucks, but there's nothing we can do.
Did your friend make any changes other than switching the gövts, or was that it? I'm truly surprised it worked. Even when considering the fact that particular flag (the one making certain ships immune to player weapons) is kinda buggy when it comes to missions sending ships in with that flag, those kinds of bugs don't involve making the immune ships hostile to the player when they shouldn't and only occur when they are meant to escort the player (meaning they show up as escorts you can command, not normal ships).
This is all very intriguing, I've never heard of a problem like this before. Also, you said your friend couldn't target the UE ships. This shouldn't be unless they were special versions of UE ships set to not be targetable. I suppose it's possible WinNova's Engine works differently, but I doubt it very much.
Bottom line, this doesn't sound like a bug so much as sabotage. Well, not sabotage, but something more complex than a simple error in programming.
One last note: Guy's Port is NOT and update, it is a separate version of the EVO TC for Nova. Don't use it with any other port, that would probably cause problems.
This post has been edited by DarthKev : 13 June 2010 - 11:14 PM