I am very familiar with this functionality, because I really like being able to toggle "always on top" on/off for any window that I want, when I want. I searched far and wide on how to do it, and you simply can't directly via Windows. It has to be done through scripting, via AutoHotKey for example, or a GUI app that has the "always on top" toggle functionality built in, for example Stardock's Windows FX.
So... Music Bringer, have you ever installed a GUI specific program to enhance the appearance/usability over stock Windows? Stardock programs are certainly a strong candidate, but there are a ton of programs out there that could be the source. Even if it seems unlikely, it may have "always on top" as one of its features, which you may have accidentally activated for MC.
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On a side note, to address my desire for total control over "always on top" functionality, I personally use a program called StrokesPlus.net, which has a mouse gesture built in to toggle always on top. I personally have 50 different mouse gestures programmed in to launch a plethora of common tasks (cut, copy, paste, escape, undo, redo, save, reload, maximize, minimize, restore, show desktop, etc., not to mention 20 commands specific to MC).
It is impossible to overstate how spectacularly useful this program is. To top it off, it is FREE (he does accept donations however), updated regularly (like multiple times per month), and the developer of the program runs a forum that is amazingly responsive to all queries (directly from the developer himself, who is a one-man operation). I would paste the hyperlink, but I don't want to violate any forum rules… Just do a search on strokesplus.net.
If anybody does decide to try this program out, I would be happy to provide my config file that I've optimized over five years which will save you a lot of time upfront... Send me a PM if interested.