in my case, i brought both my 50D and 5D2 to the F1, and 5D2 did much better than my 50D in AF locking and tracking. ended up using the 5D2 most of the time. >90% 5D2.
the shooter beside me had a 5D2 and a 1Dm3. He ended up using the 5D2 most of the time over the 1D3 as well from what i noticed.
I think this says alot about the focusing ability of the 5D2. I would tend to think user error in your case. As others have said, did u focus on the edges of the seat or just bam at the centre of the seat?
my F1 thread for reference
http://www.clubsnap.com/forums/showthread.php?t=580276