Having not really looked at the script, I might be wrong - but it kind of looks like the windowskin itself is semi-transparent, which means that even if opacity is 255 it will still be see-through, and I think it might be 255 in those screenshots. Normally, viewports would be helpful here, but I think they wouldn't apply given the centralization.
I'm guessing that the only real way to fix in this case is to make a couple dummy windows to place between the dialogue and the main screen.
I might look at it if I have time, but I would maybe suggest using a more opaque windowskin if that's an option.