You could try and take the model trough Poseray, check all textures and maps and save again. Regarding transparent windows; the default shader's opacity is either black or white, no gradient. So you'd have to use a glass shader instead. But another problem is the shadow; an object either makes a shadow or not, so if you want to have the plane making shadows, but the glass oviously not, you'd have to save them as separate objects, and set respective shadows on or off.