I'd try taking the top frame off while the rest is still on the car. If the problem is there then you save the trouble of unbolting the entire assembly. If not then you're no worse off than before.
If those screws are in place then I just don't see how it can move like that. If the glass is too small then there will be room for the frame to move around, but there would have to be enough force to bend the L-brackets. I'd think this kind of force would have a fairly obvious cause.
The fix may be as simple as loosening all the screws, jiggling the frame around until it settles, and tightening everything up again. Just beware of disturbing the glazing if you move the frame very much over the glass.
If you find yourself up this way, I'd be happy to assist.