The "some channels not coming through" has been traced to a cable card authorization / pairing error every time for us. One of the keys to finding the problem is looking at the "Authorization" value which deals with channels that require encryption. Its found on the "Conditional Access" page.

This exact problem is the reason I no longer sell Tivo products. A Tivo install can take hours, or days, to complete; relying on the capabilities of the support personnel at the Cable Co to help you. It is impossible to accurately quote the labor needed for any Tivo job, because you don't control the outcome.

There is really helpful support on the Tivo page however.
[Link: support.tivo.com]