It sounds like the transparency of the top layer is the issue, right? Are you sure you've got the .outTransparency of the paint image connected to the correct .inputs[#].transparency of the layered shader?
My instinct would be to work with simpler formats (i.e. not PSD) to get to the bottom of this. Use a simple colour image for the paint spots, and a greyscale image for its transparency (remember, white is transparent, black is opaque, and grey is semi-transparent).
Since the paint spots are also blinn, a simple grayscale map in the transparency channel seems to have done the trick. The window looks right. No layers needed. Thanks for calling my attention to it. (Any normal person would have tried this first).
Of course, I'll eventually have to revisit my layered shading problem. I can never seem to get those working properly.