Hi 
Yes, it is clear what you are talking about.
In the linux world we call the "windows explorer window" a "file-browser
window" or just say "file-browser". It is quite different from a
web-browser of course but also has some similarities. In the file-browser
you browse the files and folders on your machine or in network
file-shares. Windows tends to force you to stay with their own one but
even in Windows it is apparently possible to use a different one. Most
Operating Systems have a default one but then allow you to add a different
one if you prefer. There are tons of different ones of each (Thunar,
Dolphin, Nautilus and on and on for file-browsers) so it helps to use the
generic word to cover all of them.
I think the problem you are having is a Windows problem rather than a
LibreOffice one. Is it happening to other sorts of files and other
programs? Even if it is only happening with LibreOffice you might still
find it more useful to ask Windows Support places.
Generally any window (or console) has a title-bar at the top that shows the
name of the file or folder showing in it's window. If you right-click on
that then you get some weird options such as "Minimise, Maximise, Move,
Resize and crucially "Always on top".
If that option is ticked in your file-browser then it would makes sense
that it's staying on top of other things. Just untick it by clicking
anywhere on it's line.
It is possible that your version of Windows might have a "Always
underneath" type of option although that kinda sounds a bit of a mad option
to me. So it might be worth right-clicking the title-bar of an open
LibreOffice window jic.
Regards from
Tom 