How to disable Energy Saver mode when switching to battery to stop background windows hiding?
The problem appears to be Parallels Toolbox. To turn it off, you have to go into the settings for Parallels Toolbox, which is in the upper-right of the main window for it, then uncheck Energy Saver. There are about 2 other areas with energy saver options, but they just turn it on/leave it on.

Hitting Cancel on one of the other screens tricked me into thinking it was off, so ensure to follow instructions above.