Thanks for the resource Sree, I have bookmarked it and emailed that to myself for when I'm on another computer.
I have just tried out v4.4b20 and I get the same result when using the "best" setting for the render:
rendering in v20 is a lot faster (yay!)
Only the glass that was named "sweethome3d_window_pane" in the modelling software is rendered correctly, the other two (both with edited .mtl files) don't render fully as transparent, only the bottom portion seems to render that way while the top is opaque. -- see screenshot
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(Only the glass that was named sweethome3d_window_pane (the pink one on the right) is rendered correctly, the other two (both with edited mtl files) don't render fully as transparent.)