I'm having this problem as well, it is very annoying. In addition, sometimes the alpha channel won't work on the rounded corners and it makes white squares where it should show through to the desktop. I did, however, just find that unchecking the Setting "Translucent Fence backgrounds (Windows 10 only)" fixed both issues. It was worth it to pay for the upgrade from 2.x to 3.0, but please make it work right before you ask me for more money.
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