Periodically when resuming my windows session, windows would become invisible to Alt-Tab switcher. Until I discovered a good workaround I would have to ungroup those windows for them to again be on the Alt-Tab roster. I could then regroup them – until the next time the problem showed up. The problem didn't happen every time I resumed from sleep, only occasionally. This has been occurring for as long as I've been using Groupy, with me ungrouping and regrouping the problem windows sometimes typically once or more per day.
Eventually I came to associate the occasional nature with another occasional behavior, the tendency for the Google Hangouts window to sometimes jump to the front of all my windows with some kind of refresh activity. Wondering if that might be throwing off Groupy in some way, I stopped including the hangouts window in any of my Groupy groups. I did that a few weeks ago, and the Alt-Tab invisibility problem hasn't occurred since then. I'm pretty confident that the Hangouts window taking focus messes up Groupy in a way that messes up Alt-Tab visibility.
This workaround is pretty satisfactory, but it would be nice if someone at Stardock investigated and, if the Hangouts window behavior really is triggering the problem, prevent it from happening [that is, prevent Groupy from getting confused]. It would simplify how I group my windows.
In the meanwhile, maybe this info will help someone else who's seeing the same misbehavior.