Actually this is by design. After changing the gametype, you have the option to either restart the current map, select a new map from the list, or rotate to the next one in line.
The fact that eXtreme RCON is closing after hitting "apply" in the map control menu, is a safety feature. If you have PIN access enabled, you have to enter your PIN after restarting or changing the map. If we would keep the map control menu open, you risk being kicked for unauthorized access to RCON, because you are in a menu without proper authorization.
I can try to improve it, so it stays open when selecting a new gametype, and only closes when actually changings maps.
