Bristol Jonesy, Thanks but per my original post, I am switching to automated mute first so I don't think that is the problem.
Guitar Hacker, I can use fader automation, of course, but as in my original post, I really want to save that until the mix and just turn the right tracks off and on while working. Clip automation or clip mute will not work because Melodyne is in the tracks.
Basically, I can automate the faders quickly to get something going, but mute would be much more convenient and should work. I do believe this is a bug.
One thought: since some people say auto mute works, and since there is a known issue trying to use auto mute by pressing the mute buttons on a control surface, maybe something about connecting the VS-700 control surface screws up the automated mute function. To reiterate, I am clicking the on-screen buttons—not pressing the hardware buttons—but maybe this is an interaction bug between the VS-700 and Sonar.
For now, I will just use quick and dirty fader automation but I really really wish I had automated mutes for many reasons. One reason is to preserve the fader moves while deciding which tracks to include in a mix—especially inmportant if you are doing multiple mixes.
Thanks for all the replies.