Quick update:

I found a couple of people on the TiVo community forums having the same exact issue that I am.

I did some further testing:

With my 970, I have no problem playing ANY recording or live TV audio stream, PCM or Dolby Digital.

I borrowed a friends Denon AVR-987 receiver and it does not exhibit this problem either.

When the issue happens with the 990, changing inputs at ANY point in the recorded or live program fixes the issue and restores audio.

I have reported this to Outlaw CS. I think this likely points to an issue with the 990 locking on to the signal rather than an issue with how the TiVo outputs.
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Outlaw 976, Outlaw 7700, Pro-Ject Phono Box S
Sonus Faber Domus Grand Piano (F&C), Niles HDFX (Surr. & Rear Surr.), Outlaw LFM-1 Plus, Velodyne SMS-1
Sonos multi room audio
Video: Sony KDL-46V2500, OPPO BDP-103, TiVo Premiere XL4
2-channel: Outlaw RR2150, SF Concerto Home, Outlaw LFM-2