text: I live in your area and use a TivoHD with FiOS. I don't record The Simpsons, Family Guy, or American Dad, but I do record House and 24. The audio on both shows was fine.
  Are you using your TV speakers? If so, make sure you sure you have the TiVo's audio output set to PCM:
  The default audio output on the TivoHD is Dolby Digital. Some TVs can accept and decode a Dolby Digital signal into stereo, but they have trouble handling interruptions in the DD signal. You can usually restore audio by using instant replay. Setting the TiVo to output PCM (as above) should eliminate that problem.
  If you are using a A/V receiver or HTIB, then it is possible that your unit has trouble handling breaks in Dolby Digital signals. This issue is not uncommon in HTIBs produced prior to 2006 and A/V receivers produced prior to 2004-2005. When you lose audio with these surround systems, you can usually restore it by hitting instant replay. If you wanted to eliminate this issue entirely, while still maintaining DD5.1 audio, you'd probably have to upgrade your surround system to something more recent.