I think you might find all pools are above the jump off point. When there are no other suitable pools bitHopper defaults to XXPPS type pool until a better pool is found.
I thought that was the problem at first, which is why I cleared out the stats (deleted stats.db)
When I restarted bitHopper it showed 0 stats across the board.
Wouldn't this make it choose one of the "mine" pools over the "backup" pool?
Or am I misunderstanding bitHopper?
Yes, you are misunderstanding bitHopper i think. Let me rephrase my last message: All proportional pools are above about 700000 shares total. This makes them unhoppable, so we go to backup. Backups are PPS or a PPS variant , meaning you get paid for every share and have an efficiency of 1.0
So I'm mining a backup at the moment, too.