Setups consisting of a DOORS 9.6.x client and an older DOORS 9 client installed at the same time on the same machine are not supported by DOORS and will prevent document generation.
The problem is that the DOORS 9.6.x client installer does not does not remove the old version so unless you manually uninstall it yourself you will end up with an unsupported setup. Quoting from Upgrading to a new release of Rational DOORS from an earlier release of version 9:
If you are upgrading to Rational DOORS client version 9.6.1 or later, you must uninstall the previous client by using Windows Control Panel Programs and Features.
This is relevant to RPE as parallel DOORS 9 installations prevent the DOORS COM API from functioning correctly which in turn prevent RPE from getting data out of running DOORS instances.
The symptoms range from RPE failing to extract the data to run-time errors as described on the RPE devWorks forum here DOORS 9.6 64 Bit run-time error.