Well, here's a similar issue. I had Start 10 v1.56 installed on my spare PC and it worked fine. I upgraded it to Start 10 v1.60 and no matter what I do the WB skins start menu will not apply, it is always the Windows 10 menu.
So I gave up finally and went back to v1.56 and all is fine now. I have tried everything, even set the settings exactly to my main PC's settings for v1.60 that works fine with that version.
Looks like Start 10 v1.60 has some issues for sure.