First of all, do the above. Do not make a texture transparent unless you want it to be painted.
I don't know how to do this in ms3d, but in Blender:
Select your windows
Separate them so that they are a separate object/node/mesh from the rest of the car
Create an empty object
Parent the windows to that object
Also, separate all of your non-paintable materials from your paintable ones, but don't parent them to anything unless they're translucent too.
Why:
If your shaders are off, even if everything is textured properly, if any material is in the same mesh as a paintable material (transparent texture), they will be colored when the color changes
If translucent materials are in the same... area as opaque materials (i.e. NOT parented to something), the opaque materials will have a tendency to act like this:
