Ok, I have found the problem (although I would still appreciate some help).
The application is INSTALLED by an ADMIN.
The application is then LAUNCHED by restricted users.
It appears that the application does some "registration" when it is first launched. This includes adding many registry keys to the HKCR area. It seems that without these registry keys, the CIS part of Capture does not work. However, the restricted users do not have permission to allow the program to write to the registry and therefore it never works.
Does anyone know if there is a command, or program that comes with Capture, that will register the program correctly without actually running Capture?
Since our installation is silent as part of a distributed automated install, an admin never actually touches the machine and therefore can't run the applicaiton. The only other option I have is to "record" all changes that the application performs when it starts, and distribute these accordingly.
Note - we already open permissions on the Cadence installation folder for restricted users.