After descending below 10k feet I hit CTL-F12 to choose the airport and gate. GSX pops up and just keeps spinning. I go to restart GSX and when I hover over the icon it disappears. Then after restarting it again I can choose the airport and gate.
Several users reported Couatl quitting in flight, but we haven't been able to reproduce it so, we would need to have more data about which add-ons you are using, the airplane used, the route taken, etc.
In any case, the Couatl program has been designed to be started and restarted at any time, so starting manually, even if might be slightly annoying, won't cause any issues to it or the simulator.