Okay, it looks like my guess might be right.
Try giving your window a "thickness". Right now it's one dimensional, so your glass won't model correctly.
Also, when working with skindigo you have to make sure all your faces are pointing in the right direction. To check which "direction" it's pointing, first click on the monochrome sketchup style. Any face that is blue is currently counted at "inside out". I think skindigo doesn't like that, or at least it didn't used to, so keep all your faces straightened out.
Here's a link to your file after I messed with it, so you can see what I'm talking about.
You also may want to read up on exit portals. It looks like you were trying to make regular old transparent windows, but exit portals may suit your purpose better if you don't care about seeing anything outside that window.