I've been successfully using my 990 with my Tivo Series 3 since Gonk helped me with this back in February. Maybe I'm missing something in your thread but I had the same problem your describing when I had my Tivo output as Dolby Digital. Once you change the output setting from Dolby Digital on the Tivo3 to PCM it eliminated ALL audio dropouts from the Now Playing menu.

Palmer you state in your second paragraph that your Tivo3 is set to Dolby Digital, this is what needs to be changed to PCM. I bet once you correct this feature you'll be good to go. Hope that helps.