When I load my sim to a senario, the GSX green bar pops up as normal, but its position is half way down the screen and not at the top as usual. GSX works fine however, so I am not to bothered, it just struck me as odd.
What you are looking at, is not "the GSX green bar", meaning it's something specific to GSX. Is the standard green bar for messages, shared by all Simconnect applications and, same as with the menu, no application has any control over it.
What might have happened, is that you might have undocked it at a certain time, then moved it, and docked again, so the sim saved its position. You should be able to fix this by undocking it again, and move it back on top of the screen so, any application (including GSX), which use the Simconnect text window, will have it in the proper place.