I am curious as to why this program would disrupt the operation of GSX and whether it might be this particular addon that blocks GSX or if any such program that keeps a window on top would cause the same result
We'll might check that program but, in general, is a very bad idea having a program that forces its windows to be always in foreground. What about if *two* programs would try to do the same ? The windows system would become quite confused, with a lot of conflicting messages (a program must send a message to Windows to be put into the foreground) being sent between application.
With GSX, this will surely disrupt its user interface, since it's made with dialogs that are being put on foreground *just* for the time they need to appear on screen, and such program will likely prevent it to work. The same with the Addon Manager and with any other FSX add-on that will need to display a standard Windows dialog at some time.