I was having the same issue myself, and i know about the settings for the DD -> PCM within the Tivo box. My issue is this however:

The 990 only outputs a dolby pro logic signal, i can not use the DD 5.1 signal. Once i change the tivo back to just DD, 5.1 works fine till i change the channel or watch something recorded. Then i am back to no audio till i unplug the connection or change the tivo back to DD -> PCM.