that's interesting; presume you have the auto roof, Is it still not fitting with the roof down?
not had any problems with the windows since getting the car 12 months back, but, it reminds me of my last car (15 years of MX5 ownership; Mk1 & Mk3).
the Mk3 roof came down slightly off line once & pushed the window out of line. It's just a random thought that may or may not help.
be interesting how they fix it.