A Dexpot rule was the first thing that came to my mind too. I didn't think to check that it could be the progam itself though! Thanks. I'm not sure how one day it started doing that but I found out how to disable it.

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the checkbox doesn't necessarily mean it's been set by Dexpot.
Do you have a desktop rule enabled?

Whenever a video is played using Media Player Classic, this window is set to be "always on top". If I inspect the context menu, it will show the checkbox next to this setting even if it was unchecked the last time Media Player Classic was closed.

Also, if I manually uncheck this box then I can successfully navigate away from the active window once without it coming back to the top. But once I reactive this window, the setting will have reset itself.