Hey, i did a clean instasll.
The Default Themes you have i found that some do no longer have this problem, but those i list here still do.
The Captain (No Problems)
Modern (No Problems BUT)
Modern - with blur (Preset) (Got problems)
Echo (No Problems)
Decisive_Win10 (No Problems, but the win 7/8 dos)
Corporate (No Problems)
This is how it looks, as you can see the "box" where the menu is in, is transparent, i can see Blinds interface through the skin.
https://i.imgur.com/ZVjgsOh.png
Altho, i did see some of the default skins, have a blurry transparent "box", but im still unable to find where it is in the SkinStudio.
https://i.imgur.com/C9I7ca8.png
Made a little video, if 1 image say 1000 words, then a video will say well a lot more 
As you may see the Them Captain for Win 7/8 i cannot even apply to the desktop, the Blind just simply refuses to apply it, also it dos not even show a preview right, but well, not the main problem for me tho
As the video was taken, i did have installed my theme i wanted to use, to see if it had changed, or i could find a solution, which i still have not, have tried to see what the difference between those that work and the other are, but simply have not found out yet. :/
But i have found a annoyance in the SkinStudio tho, when ever i do anything, the mouse cursor moves to the right of the screen :/
This makes it a lot harder to do anything, since i have to move the mouse to the middle every time i do anything.
This is with DARK colors in Windows (Settings > Personalization > Choose your default app mode > Dark)
