There was a similar issue posted recently about the Hopper 3 and Vizio TV's and/or soundbars. (I saw the same thing happen with my ViP211k and my Vizio TV.) Tampa8 posted a solution that seemed to help reduce my audio sync issue:
This issue started about a month ago. We use the pause one tuner and swap to the other feature quite a bit. We started noticing the audio would get out of sync with the video. If you paused or clicked the back button a few times, it would fix the issue. But now it's doing it A LOT and sometimes...
www.satelliteguys.us
The audio settings he references are for ViP receivers, but there are similar settings on Hopper, as you can see farther down in the thread. The key seems to be turning "Volume Leveling"
off. Another key is to not turn on your Dish receiver until right before you begin watching TV, since the delay seems to get worse the longer the receiver has been left turned on.