Are you using L or ML? I'm getting the impression that they broke some aggregate device functionality and also sync. E.g.
https://discussions.apple.com/thread...art=0&tstart=0
https://discussions.apple.com/thread...art=0&tstart=0
Opposite experience:
http://www.gearslutz.com/board/music...te-device.html
However, AFAIK even with Slow Leopard the aggregate device didn't always work with all interfaces.