Well, that didn't take long. I've done the cleanup, rebooted, reinstalled, and just as I started to get back to work I switch to a different virtual desktop using Ctrl+Win+RightArrow and get the following again. Reminder that I'd uninstalled Start11 previously and ran without it for a few days to have this issue disappear. Then I reinstalled it and the issue returned. I was hopefully your cleanup script would do some magic but it doesn't appear to have helped. I really want this tool to work as I really like the start menu and taskbar customization capabilities; they're great. But between this issue and the fact that clicking on a running program in the task bar doesn't work sometimes until you click the Start11 start button and some of the other GUI issues such as the right-click menu hanging in the Start Menu, it's just taking up way too much of my time trying to figure out all the bugs.
I would also like to point out that this Windows 10 install was done this month. So this is not an old Windows 10 install that's been upgraded from a prior Windows version or even a prior feature release. It is the latest version and it was installed as the latest version. I do use FancyZones, which is a feature in Microsoft PowerToys, to simplify my 49" super-ultra-wide and a couple of other 24" standard ratio monitors. And PowerToys has also proven to be buggy. I suspect these issues 'could' be associated with running both PowerToys and Start11 simultaneously. At this point though, it's more important for me to have FancyZones than a fancy start menu.
I'm not going to ask for a refund but will instead remain hopeful these bugs will be squashed in the near future where I can try again. Please let me know if there's anything I can try or anything I can do to help track these down.
