First, check your signal strengths; we have to assume they are good.
Second, try turning Dolby 5.1 off and see if the problem can be narrowed down to a DD problem.
Third, change channels and listen for dropouts (this puts the DVR in a "direct-through" mode where the HDD is not in the chain). Then pause and unpause (invokes the HDD) and see if the dropouts are there. This will determine if the HDD is involved. See if the dropouts are in the same place on multiple playbacks of the same scenes. Are there any video disturbances associated with the dropouts?
Finally, try a restart.