This issue occurs on my PC whenever I run Clover. I've emailed the developer about it twice, but haven't heard back, so I thought I'd ask if anyone else has had a similar problem (perhaps with a different program) and found a solution:

When I first run Clover after starting up my computer, taskbar thumbnails do not appear correctly on my computer. If I quit Clover and hover over some taskbar thumbnails, then they appear correctly. Usually, when I run Clover again, my taskbar thumbnails continue to show correctly, but sometimes the problem reoccurs and I have to once again quit Clover and hover over some taskbar thumbnails to fix it.

 

I finally uninstalled Clover because I was frustrated by this bug and how often the program made Explorer stop responding, and it appears that it's no longer developed. I switched to QTTabBar, which I previously disliked because I felt it was bloatware, but I'm enjoying using it so far.