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When it happens, I simply change the channel, and change it back, and get the sound. At that point however, I occasionally lose sound when it goes back to the national feed, and have to do the same thing. Very frustrating. Does not happen on my Contour DVR, only on my second box.
Try different sound settings on your TV or sound system. For example, if you're using Dolby, try switching it to PCM when the audio cuts out.
Also, what kind of box is the "second box"? Is it a smaller host box for the larger Contour DVR or is it a separate box like a HD box? Or is it a mini box? There should be a model number on the back of it, or you can describe it in general.