Michael - As has been pointed out, you need to connect your Dish DVR to the audio system via optical cable to get true 5.1 DD. Or, if your audio system has HDMI inputs and outputs, use HDMI from the DVR to Audio system, then HDMI from Audio system to TV. As you, yourself, point out, the Sony amp is only synthesizing surround sound using its ProLogic decoder, which might be what's causing the issue.
Also, make sure the Audio settings for the 722k are set for PCM/Dolby, Leveling Disabled, and Line. THat will give you the best audio quality from the DVR.
Obviously, with the above hookups, your TV remote will not control the volume. You will need your Audio system remote to control the volume. But, you should not be using your TV remote anyway. You should be using the 722k remote for the DVR, TV, and Audio system. (And, DVD/BluRay, if applicable). Or, better yet, get a Harmony 650 or 700 to control everything a bit easier.