If you can't tell any difference in the 7842 output wave forms when you switch inputs or free run then I'd think the problem was down stream in the processor. IT is possible depending exactly when the transition occur in relationship to the syncs the down stream processor may be having problems when the syncs don't follow the standard pattern.
Many of the undocumented registers are internal counters and such that the chip designer mapped to external access so he could get a look at these values during initial chip bring up. They generally serve no purpose in the production environment.