I know the door panels from LMC state they aren't direct replacements, so I'd guess if they were "cast" wrong, with the window seal exerting a lot of pressure on the window as it goes up and down, then that could be a problem.
I'd suspect more likely that the tracks or regulator mechanism is messed up, but pulling the door panels back off should let you see whats going on inside fairly well.
Did you have any problems before installing the LMC panels, and if you didn't, did you have any problems while changing the panels, that might have affected the window mechanism?