First off, great stuff. It's nice to see software working as advertised.
And of course, I've broken it. Well, not exactly. At my company, we're running Microsoft Configuration Manager software. When the agent is installed on the system, it creates a new display adapter, named "ConfigMgr Remote Control Driver." It seems benign enough, but here's where it wreaks havoc with DisplayFusion: that's now Monitor number 1. My wallpaper for the "left" monitor goes to a monitor I can't see (the configmgr monitor is a "virtual" monitor). DisplayFusion thinks it's a real monitor, and treats it like one. Meantime, my other (the actual physical) monitors get the wallpaper for the "right" monitor. In other words, I only get one wallpaper for both monitors.
I suspect this is an obscure bug, but I'd be interested in any ideas.
The bug had to do with not applying the wallpaper correctly in very rare situations, which usually ended up looking like only one of the monitors had the new wallpaper applied. Please give it a try and let me know if this is corrected for you now.