So I have recently noticed that whenever DisplayFusion changes the wallpaper, whatever program is currently the active one becomes a non-active one. I've noticed this problem for a while, but only recently did I discover what triggered it. I'm not sure how long it's been since this problem started, but at least since I started using the 9.0 beta builds, so it may or may not have been the changes in the beta build that causes this.
This problem is especially annoying for me since I have a special mouse and a pen tablet that both have custom settings for hotkeys and whatnot depending on what the active program is, so if the wallpaper changes, then suddenly my settings revert to the default settings and undesired things happen. For example, I have my pen tablet mapped to a different part of the screen when Photoshop is the active window, so if the wallpaper changes while I am drawing, my cursor will jump to a different part of the screen.

In the DisplayFusion wallpaper window, click Wallpaper Settings, and disable the "Use transitions when changing..." option

This doesn't affect the problem, and the problem still occurs while this is disabled.

On the DisplayFusion Settings > Options tab, disable the "Aero Colour Mode" option

By disable, do you mean select the "Don't change the Aero colour" option? If so, then this option was never turned on in the first place.

In the Windows Personalization > Colours settings, disable the "Automatically pick an accent colour" option

This option was also never on in the first place.

9.0 Beta 3, which is the latest beta as far as I know.

It looks like the latest beta build fixed this issue as far as I know with my limited testing of it. Awesome!
Keep up the great work with this amazing computer program!