1. On opening GSX I have a red circle in the middle of the screen.
You mean a red *octagon* stating that FSX wasn't closed properly ? It's nothing related to GSX, it's a message generate by Ultimate Traffic 2, no idea what exactly means.
3. The pushback window disappears and I am unable to open the window before the pushback truck disappears, hence I am unable to taxi and take off.
I don't quite understand this, why would you need the GSX Pushback window to be open, in order to start taxi and take off ? Taxi/Take off is controlled by the ATC Window, it might look similar to GSX, but they are two entirely separate things, with different keys.