It does sound like your AF is not up to par, but I have to disagree with the sentiment that the 500mm focuses as fast as the 400mm f/5.6
The 400m with it's terrible MFD never has to AF as far as the 500mm might have to if the focus limit switch is not set, and is known to be one of Canons fastest focusing lenses. In many situations it will be the faster of the two.
If this were the only concern, then I'd say your 500mm is fine.
However, the 500mm AF accuracy should not be less than the 400mm at all,. so it does sound like yours needs some kind of adjustment.