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I was very happy when I saw that the skin supported the PNG’s transparency. And I thought that I could use that to change slightly the shape of a window by drawing a different shape (ie square with rounded corners) in the /WindowNcArea/FrameActive.png file. But there seem to be a mask or something applied, and it forces the transparency to be only at the rounded corners, making any transparent part of my PNG white. You can see an example of what I mean at the following link: http://tinyurl.com/n5kmc9 . Gray being the shape of the box I want, and the white block should be transparent.

My question is, is this a Windows thing that we can’t change or something in Prof-UIS that we can go in and tweak? Like maybe a file that serves as a alpha channel/mask or something like that?

Thank you

This is the current limitation of window frame skin. The rounds on corners should be enough small: not greater then resizing border width/height. So, we can assume your message as a feature request.
Besides, in case of frame the transparency is supported only for two transparent states: completely transparent and completely opaque. Simply saying, this is limitation of MFC. Windows supports per-pixel window transparency. Such per-pixel transparent windows are called layered windows. They are very specific and they never have child windows (toolbars, views, status bars). Normal application always have several child windows inside each its desktop window.