I talked to a guy at a local competition about this issue this past weekend. It sounds like it is a problem with either bench or wing cappers. He mentioned making a ring out of PVC and that solved the problem. I haven't tried it yet so I haven't really figured out what the problem is. It sounds like the capper bell is too deep and the sidewalls hit the sides of the bottle before the cap is able to be pressed on.
I've been saving these bottles for a while now so I have about ten 12 packs of them with boxes in nice condition. I'm kind of bummed that it's not going to work without issues as these bottles stack up well and save a lot of space.