There's an option to view the battery level of your remote in Contour, but I've learned it's not very dependable. For example, when Contour starts issuing messages, "Your remote's batteries are critically low..." I can still get another 3 months use from the "low" batteries. I just ignore it until the remote stops working.
Anyway, the option to view is Contour button > Settings (gear icon) > Remote Settings
Right now, mine reads 0% but the batteries still work.
In your situation, perhaps the Mute command requires a higher frequency for the transmitter to generate but your batteries are at some threshold to not generate enough power. Just a guess.