Last version 8.3 (2469) x64, Windows 7, check bug on fresh install also.
I found a way to fix it till MD restart - go to menu:
Explorer panel settins → |Colors| → Background → [ ] Override standard windows background
check this option; [Apply]; uncheck this option; [Save].
After this manipulation "Highlight the background on panel in focus" start working till you close MD.
P.S. Once happened, that only in one certain tab background would not became darker when this tab inactive.