Have you cleared your cache? I recommend clearing your cache first, then check to see if it still causes the windows to get messed up. If that doesn't work, then uninstall all your mods.
Reinstalling your mods won't help, as it's probably an outdated mod causing it. Disable your mods until you find the broken one. That's the price to pay when you want so many mods.
The only mod I remember that was doing this was an extremely old version of the CrashHard Dummy back when the dummy had the same color as the car and there were random broken material files all over the place in the mod files for whatever reason. You definitely shouldn't use that version if you have it.
