While I am looking into this (unlikely that you will see a new version before next week, because tomorrow is the day we celebrate our independace from King George III.
1. What is behind the window. If it is a SketchUp Sky, or a background color, rather than an Automatic or HDRI sky, then the transparency will may not work.
(I thought we had fixed that, but it may have broken again)
2. Does the material appear transparent in the Material Eiditor?
3. Does the material have a texture. (Some dark SketcUp materials have a texture which is black. Because nXt defines black as a color which doesn't let any light through no matter how transparent it is, we have a problem with black textures in materials)
4. Copy the window to the clipboard, paste it into an empty model, and send it to me.
(It is so much easier for me to test things with a small model)