A picture speaks a thousand words, Sojiro. Can you show us an example?

Thanks for the information people. Shame to hear that it isnt really a bug. But, I did made some screenshots to show what I mean. The first image is a theme that aligns perfectly and the other aligns weirdly.

"The perfect theme"

"The misaligned theme"

As you can see, the top window aligns with the top but there is a small gap to the left and a bigger gap between the windows and the bottom window. I aligned them in the corners with WindowFX to make sure they are 25% of the corners.

So this is really a designers choice?

I believe your screenshots are a fine example of Lightstar's explanation.  If you look closely at the images, the top skin has no shadows and the bottom skin does.  Those shadows are built into the window frame images and they take up space on the screen, even though part of the shadow is almost completely transparent to provide for a smooth blending out.  So, when a designer chooses to build shadows into the theme, which is typical, the window will use "extra" space for those shadows.

On an older version of Windowblinds, in the WBConfig window (where you select skins), there is an option in the "Settings" tab which can be selected - "Do not use Per Pixel frames even if the skin supplies them."  I don't know if that option remains in the current version or how it might perform on Win7 or Win8.  It will make WB use a second set of frame included in the skin, UIS2 frames.  They will have very little or no transparency, and you can not use the WB transparency adjustment on them, but using that might be an option to accomplish the effect you're wanting.

Thanks for letting me know it's still there.  I really didn't know, it comes up so rarely.