Never mind, we finally got it figured out...had to manual create some registry keys, and have both 10.1 and 10.2 License managers running. Hopefully 2013 will run with the 10.2 license manager.
I also have this problem, and could you tell me how to manual create these registry keys? Many thanks!
it could help if you install the patch http://support.esri.com/en/downloads/patches-servicepacks/view/productid/186/metaid/1929 which was created for the combination ArcGIS 10.0 / CityEngine 2012. This patch helped in various incidents for the combination ArcGIS 10.2 / CityEngine 2012.
It has to do with the information about which version number is included when authorizing your software - you can check that by opening an authorize.txt.
Compatible versions are:
CityEngine 2011 / ArcGIS 10.0 -> authorize.txt will show "version=10.0"
CityEngine 2012 / ArcGIS 10.1 -> authorize.txt will show "version=10.1"
/ ArcGIS 10.2 -> authorize.txt will show "version=10.2"
So trying to authorize a CityEngine 2012 on a machine on which ArcGIS 10.2 is installed - it will generate "version=10.2". And that one entry will lead to your observed problems of authorizing CityEngine....
Hope I shed some light into this,
Esri Germany Technical Support