Door Window Problem

[tcoop68]

I am building a 67 GMC for a friend and I have something going on I never had a issue with before we put brand new doors on , new complete windows with metal , new regulator , problem is when you roll the window up all the way the metal tract that is glued to the bottom of window come out of door way to high and if you have window rubber rain sweep and rattling strip inside installed the metal catches on it and wont let the window roll up all the way its like the window is 3/8 inch short but it measured the same as a original I have a couple of solutions but I was wondering if any of you guys ever had issues. Thanks