I think I might've been right behind you at security, assuming you were flying on Sunday?! I've been put right off Jet2's online checkin since my first use of same managed to change my name to someone else and allocated my seat to the person who's name my booking was changed to...(my suspicion is this was more likely a check-in agent was at fault, but it was worrying nonetheless). I just use the self serve checkin at AMS & rarely any significant queues at MAN to worry about...
I've never had a problem with self printed boarding cards on assorted airlines - they always get scanned at the airport, but I tend to print them on an industrial strength laser printer...