Are you using the latest version of Skype?

I noticed this to as application got own skins, add them manuel and chose ignore this application so WB wont attemt to skin them and messing up layout of the program. you see next time you start this application it will load correctly.

actual you should do that for many things, also games if you run them borderless full screen trough bordeless gaming app also makes skinned side disapear but leaves invisible border and you see parts of wall paper instead of game fully fill your screen, also solving those issues with ignoring program to be skinned.

Hoped this helps a bit.

Bump

Tom if you read Reply 6 again this person says Decisive is the only skin they have used that Doesn't have the problem.

Decisive is my skin. Didn't do anything different. Made it as good as I can as usual. 

I agree it would be nice if this person would at least list 2 or 3 of the skins that don't work. Also I would like if another one of my skins was tried. 

The only thing I have ever found that makes a frame look like his image was always easy to fix. Just close the window and open it again and it would always work after that. 

Hey, sorry for not mentioning any skins that got problem.

Skins that i tried and got problems with:
Arcrylic 7, Corporate, Diamond, Echo, Eva, Ice, Lantana, Modern, Night Shine, The Captain, Win 8, Win 8 Metro.

Almost no problem in Precision as you will see in the video below, just a little boarder.

No problem with: (the only one that i tried that i have found with no problems)
Decisive.

Reason i did not mention any that did not have problem was, i thought that every one else just "lived with" those problems and thought ah well its the way it is...
But when i came across one that then suddenly did not have any problem i figured, oh wait it can be fixed some how, but how, so i tried to change a lot of settings in Decisive, but could not get it to offset :/

Many programs do not have this problem any more, in the beginning i had problem with Skype (the new one), but that i do no longer have, but still now and then programs pops up that i do have this shift offset with, like the VLC player, i made a little video, since its easier to see then read about it

None of you other got this problem at all ?

I'm running Windows 10, but since Decisive solved the problem, i think its not the VLC and other programs that got the problem, but some where in the skins, its not many programs any more that got this problem, but as said now and then i run into a few, and it just bugs me a lot when this happens, i know its stupid but just cant have it

[EDIT]
@DaveBax i tested Spaceblue (No problem), Aspire (Problems), Aspect_WB (Problems), Christmass2016 (No problem), Flattened (No problem)

The Closing and opening is not working for me.

[EDIT 2]
If i enable "Do not use per pixel frames even if the style supplies them" i get a 2 pixel white border at the bottom and right side, 

Not sure what you men with wider borders, i'm not one that create skins, i just found one that i managed to modify to fit my needs, since i have chronically migraines, i cant handle white/bright colors that well, so the one skin i use i modified to all dark.

So would really like to know where the border is, i have tried to modify several places where i see borders, but none of them made any difference for the skin. :/

Thx for taking your time to reply.

As said its rare i find places where this is a problem, at the moment only got 2 programs where its not working right, but i can live with this (even that it bugs me tho ), thought it would had been an easy fix, but for now i will let it be, til i find another skin that is having dark colors for the most part

But thx again.