Not quite sure what the problem is that you are having.
maximize an app that is minimized in the notification bar through its shortcut
I need the app to stay open while the pc is awake but to be able to bring it to the foreground from a media center through a shortcut
That doesn't make sense to me. Do you mean the Taskbar or the SysTray? and a shortcut is to open a program (start it up) not minimise an open program window.
Mine don't behave like that. If I have several programs opened and their windows minimised, I can click on any one of them in the taskbar to open them up back to full screen and have them in forefront on desktop. Also it's not necessary to actually minimise any as they will behave like sheets of paper and clicking on any in the taskbar brings that one up to the top.