Greetings, Jpow, and welcome to Seven Forums!
Could you please try to be a little bit more specific about what type of full-screen (borderless) window or windows you are referring to? And do the newly selected window show up ON TOP of the full-screen window upon opening it OR is the full-screen window on top of the window your trying to open (obscuring the full-screen display partially)?
Some windows DO have a property known as "
always on top" which does just that, keeps that window on top...always. This doesn't really sound like what you’re experiencing though, using what little information I have to go on anyway. But when a video overlay type of application or embedded form of such a object in another window is in full-screen mode, it is, and should be, on top. It just makes practical-sense that if you have some window that is set to a particular state/mode, which is specifically designed for the purpose of covering the entirety of the screen, it should be oriented to the top of the "stack" of any windows you might already have had opened. That part seems difficult to dispute, I think you would agree.
If you use [Alt]+[Tab] OR [Start]+[Tab] during a full-screen application, it will almost always (with few exceptions) orient the newly selected window to the front of the full-screen window. It's also true that if the full-sreen window is minimized/hidden, and anoter window is restored, the full-screen should either pop-up front first or appear to refresh simultaneously with the wndow you attempted to open/view. This is either a flaw in Windows or IMO far more likely somewhat of a safety mechanism created so that you can access other windows in the event that the full-screen application becomes unable to return to one of the normal window states (Maximized, Minimized or Restored) for whatever reason. This provides a route to attempt repairing the window that is not letting you remove the full-screen flag by normal means. Short of that, you would almost be down to having to reset the system if the full-screen application becomes problematic or has unreachable controls. (with the hopeful exception of task manager:[Alt]+[Ctrl]+
, or trying to exit the full-screen mode via [Esc] or forcibly close it using some key sequence such as: [Alt]+[F4], etc.- but these tend to not work well when we actually need to use them to, or so it seems!)
So, yes, in the Windows 7 sorting-order for windows the one that you have just restored or opened should come to the front in most cases when all windows have been minimize, such is the case when you use the “Show Desktop” taskbar button but the full-screen window, which is still in a minimized/hidden form of a FULL-SCREEN window will always be like an overlay that must be restored before another window can pile on top of it.
This IS normal, and while it might be less than ideal for your particular situation, I assure you that it can be reproduced easily on any Windows 7 operating system. There may be SOME way to "fix" this by somehow altering Windows 7 sorting algorithms within windows itself, but I've never heard of such a monster, and I would advise not allowing third-party software to alter your system files or mess with the registry to try to change this sort of thing in any way to be honest. You'll more likely be dealing with a more serious problem sooner or later if you allow these types of changes to take place. Hopefully, it's just a strange inconvenience to you and it’s not causing any actual disruption in your ability to preform important tasks. In which case, It's my opinion that your just going to have to deal with it as best as you can - assuming no one else has any other advice, that is.
I'm sorry I have no solution to your issue but I hope you might have a little better of an understanding of why it is occurring in the manner with which you seem to be describing to me.
Thanks for asking your question! 
Mike
