While the Orc AI is amazing, Prophets and Guerilla fighters run when you approach them etc...I believe the same AI script causes them to see past invis. I was just fire balled, shot, repeatedly while I was in invisibility. And No, I didn't run past them!
I was thinking if you could find a way to stop the crazy invisibility bugs. <.<
I can second this one. Not from being a target, but from witnessing them firing on an invisible ally from about a tile and a half away.
Hit stealth when you're invisible, it often ends the bug of them perma seeing you while invisible.