Using "allow the mouse wheel to scroll windows under the mouse cursor that aren't focused" with DisplayFusion Pro v6.0.0 beta 7, it scrolls the unfocused window... and the focused one at the same time!
I'm quite sure this didn't happen until previous beta...

Edit: this happens if Filezilla and Foobar are the focused one, I cannot replicate the problem focusing on Opera, Outlook or Windows Explorer

Edit 2: it even happens if the focused window is Media Player Classic - HC