In fsds 2 make sure your windows are the last parts in the build list... for example, select all your transparent parts (including prop disks) hit ctrl x then ctrl v to paste em back in. then when you compile the model, make sure the box for autosort parts is UNCHECKED.

I use the material to set my transparent parts. for most glass I use a medium gray with and alpha of between 60 and 120 (depending on what I'm making) with a very bright specular power.

unless the windows are curved, using a texture with an alpha channel to make them reflective has wierd effects.

Brian