2000 Mustang Convertible Window Alignment Issues

I have a 2000 Mustang Convertible. Recently when closing the door, the window began hitting the convertible top. I had to manually feed the window under the top's lip, insert it into the rubber, and then push the door completely shut. I took the car to the dealer and for $500 they replaced the window. They told me that there is a piece at the bottom of the window that broke off and wouldn't allow the allignment screws to adjust the window properly. Not less then 2 weeks later the exact same situation is occuring on the passenger door. Does this seem reasonable? Can anyone offer any suggestion other than to replace another window?

Thanks for your input...

Scott

Okay have you tried adjusting the convert screws in the front? and do you always roll down all four windows before putting the top up or down? also I don't know for sure but in the back where the convert motor is there might be two screws that you can adjust, mabe look in the manual.