[alansplace]

I only get 'some' of the channels to show up, meaning some channels are not be decoded (gray screen nothing on it)

i believe that's what you're supposed to be looking for when the 'instructions for cablecard installers' that comes in the TiVoHD box say in item 9:

'be sure to test the customer's encrypted channels'

i'd say that your installation of whichever cablecard is misbehaving was not completed properly.
--
Alan