I'm having the same issue as user:
gabhan@gabhan.com
This is also happening to me, and i'm not sure exactly when it started. But it did not start at the moment i installed VLC 3.0.3. It took some time after that.
Actually it started right after both Fences and DisplayFusion released new versions. So i suspected Displayfusion, and i even talked to the creator on his forums, and he tested it and could not find anything wrong.
After a short while it just started working again, all by itself. Then another version of Displayfusion released and the always on top started failing again.
Does anyone else here use Displayfusion? or is this a coincidence on my part?