WindowBlinds has always set that colour so I am confused as you are.
System colours have always been part of a skin since WB1.
The only thing I can think of is WB has to reapply colours should the OS change any of them which can happen after say a sleep. Should something be triggering that then the colours get reapplied.
Also be aware the desktop colour is extremely rare to see as typically a wallpaper would cover the entire desktop. You would only see it with centred wallpaper or fit to screen modes where the wallpaper is a different shape to the screen.