Solved! Go to Solution.
In the CityEngine.ini file which you find in the program's directory, add the following line in a text editor:
-Dagol
This should ignore any AGOL timeout and start CE immediately, though the AGOL features will be deactivated that way.
Matt, does that mean I won't be able to export CityEngine scenes to ArcGIS Online if that line is added to the .ini file? If so it's a workaround but will this issue be solved in a future patch?