I don't use Acrobat. (I prefer Foxit, which uses tabs but that isn't the issue here). I use groupy almost exclusively with Windows Explorer (folders). I generally have a lot of folders open at once, hence the reason for grouping them together.
For me, the issue occurs when switching from one folder to another, particularly after more than one folder to folder click. It doesn't happen every time but it is pretty consistent with how often it happens. It may happen more often with the left-most folder, though clicking to other folders will cause it to happen as well. When, it happens, the Groupy set of folders will be placed behind whatever application last had focus.
I am currently using Windows 10 1.709 and Groupy 1.18
