This happened yesterday.

I've found I tend to get a CTD when a faction leader dies (in battle or in bed). My Lussotannan FL died of old age and sure enough CTD on the next battle. I re-loaded and his stack (with the new FL in it) was suddenly invisible but still laying seige to a reb city in Galicia. I ran another FM into the stack and bingo cloak was off again.

Maybe they had the "Klingon" ethnic trait?