Jeremy, try putting the AJA card in slot #2, so your configuration would be:
Slot 1: Video Card
Slot 2: AJA LHe Card
Slot 3: Empty
Slot 4: ATTO Host Card
I had the same issue last year and moving the AJA card up one slot solved my problem! Here's a link to my original thread:
http://forums.creativecow.net/thread/4/861853#861853
Hope this helps you out!
Jason W. Tower
Fiddler Films
http://www.fiddlerfilms.com