What kind of track stack is it? A Summing Stack or a Folder Stack? If it is a Folder Stack, it's possible the output of the track that is not muting is not routed to a shared output. Are there regions on the track that is not muting?
Good question. I haven't stopped using track stacks. I just haven't been doing any projects lately where I've needed to use them much. And even when I do, it's been mostly in the basic way (layering a few different sounds).
I'm falling in love with with a caveat: I have this rather large project with lots of tracks and lots of takes.
I was hearing the lead singer where no region existed, nor were there any Melodyne blobs. I searched my stacks withut success. It took a long time before I found it, inside a 'hidden' violin stack. My mistake, of course, but wouldn't it be loverly to have a single command to open all stacks with a single command?