I have complained to TiVo about the back-to-back shows on the same channel tying up both tuners, and they have replied with the usual lame suggestions. Hopefully they have lodged it with the software developers as a 'to do' as I as I asked them to. Would you mind filling out a support request on the website too, so they might give it some priority.
I am about to replace the PROM chip on my TiVoHD so that I can hack it and install EndPadPlus. It is far more intelligent than the autopadding built into the TiVoHD. It looks at what you have schedualed to record and intelligently pads the shows.

The main reason we bought a TiVoHD to compliment our Series1 was becuse of the dual tuners. Not as good as expected...especially from TiVo.

Three months ago I had an issue with some shows being scrambled, or no sound. I happened intermittently for about 2 weeks, and has never happened since.