I'm playing campaing second time now and whenever I enter church there's a cloaked ceph just standing there. I think he should be somehow scripted but he's just standing still. He cannot be killed, I've unloaded all my bullets on him and he's still alive. Some script glitch? Anybody encountered it too?

I also had this problem on my second try though just before he ran away i fired a JAW at him and then as you put it he stopped and wouldn't move at all and wouldn't die even after i blew 3 C4s 2 more JAWS and all my felines and then another 3 minutes of punches.

I think its scripted - ie, the only time you are supposed to kill them is them is the 4 at the last mission.

I emptied a whole HMG belt into it and nothing happened

Well, but I think he shouldn't stand there making noises and taking our bullets - I think he was only there to scare you for a moment and then should run away - I think he's bugged atm.