When I had my A1200 in a Micronik tower (I don't have any A1200 hardware any more now), it was very flaky with things disappearing like that. The only thing I could do was shut down the whole system and start wiggling cards around. Either that or remove and reinsert whatever is missing. Eventually, with enough wiggling and moving, everything would start working again. Then I just had to make sure the tower stayed perfectly still and nothing bumped it.
