I don't think that is a malware problem. I had the exact same problem with my Rocket Dock for a while. i always had to unhide and rehide it. Then it would function for a while until the next time. One day the problem went away all by itself. Now since several weeks it funtions perfectly. Never found the cause of the problem.
Btw: if you want to pin a page to be always on top, you can use DeskPins: Elias Fotinis DeskPins :: Make Any Window Topmost
I would re install if it was just the dock
but windows media player is also having trouble staying on top
so I think it's more a problem with windows recignizing the comand to stay on top
yet the botom taskbar is working fine
Under what conditions does the media player not stay on top. When I have the WMP open and then open another window, it disappears too. That is normal. You can always find it in the taskbar.
right click on WMP and look for "Always show Now playing on top"
when that is checked it will normally STAY on top no mater what is done
but latly when im working in IE with it running after iv loaded a few dif pages then WMP will disapear under IE
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