Hey Hammer, have you measured the bags all over and compared the measurements of each bag? Like the distance of the rail slots (underneath the bags where they "rest" on the bag rail mounts) to the front/rear/side edge of the bag. And also the cutouts. And widths and whatnot of the bags to atleast eliminate the bags being the culprit before you start modifying things on the bike to fix it. I'm sure the bags aren't the problem, but there's no point in spending hours trying trouble shoot the bike if it's in the bags.
Fatguy