Aha! Now that I know shadows are at fault, fixing it wasn't too difficult. In the other thread, you suggested disabling per pixel frames. That will certainly alleviate the problem, but it also removes other per pixel frame functionality like glass/transparency, and it's not necessary to take such drastic measures when you can disable just the shadows. Here's how I did it:
First, make a copy of the theme in SkinStudio to use for editing. That means the original skin will be left untouched and should hopefully avoid the overwrite issue ALMonty pointed out.
Second, in the new copy, "Edit Titlebars and WindowFrames", then "Edit per pixel frames". Then, in tree view, go to "Window frames" -> "Per Pixel" -> "Shadows".
Then, for "Shadows" and every entry below it ("Top shadow", "Left shadow", etc.) go to the Image tab and change the "Image" dropdown to "No Image defined - section may be optional".
Save the skin and apply. There it is: a copy of the Win8 skin with shadows disabled, but all the other nice per pixel stuff like glass effects still working. Now that the shadows are gone, the issue in OP no longer occurs.
It's a pity; the shadows were rather handsome. Maybe there will be a fix someday. For now, this will get the job done without affecting the overall look of the skin too much. Thank you for pointing me in the right direction!