Unfortunately, it appears that those who registered while email verification was on still need to to verify thier email.
I really have no idea why this would be happening. Do you have mods installed or is everything stock. If everything is stock I would recommend simply reuploading everything. If you have mods installed, which mods. Well, I guess it is pretty obvious looking at your site that you IIP installed, but those are minor changes that shouldn't affect this. So if you could list any other mods you have installed or let us know if it is otherwise stock that might help us track down this problem.