I don't know if this is it but check the channel at the base of the window... as I recall there are two "rods" that form an "x" as part of the regulator and they have rollers on the ends... make sure both rollers are properly in the channel at the base of the glass.
When I did the windows on my 56 I recall it being a pain in the butt to keep them in place while I was reinstalling. This may not be our problem but off the top of my head it's worth checking.
