Welcome to the forum.
Do not know if this is your issue, but other users, and on several versions of PrE, have had issues with both the Soundtrack and Narration Tracks.
In nearly every case, moving the Clips from those two Audio Tracks, to empty, regular Audio Tracks, say Audio Track 2 & 3, has cleared up their issues. Not sure what the problems with those two Fixed Tracks is, but they seem either Project, or Asset dependent, in that often they work, as anticipated, but often they just do not.
Have you considered lowered the audio level or even deleting the audio from the clip instead of muting it?
Muting isn't really designed to be a permanent setting. It's just so that you can preview your video one audio track at a time.
Reducing the audio level to zero or removing it completely is really the way to permanently remove it from your project.
It does not matter if I lower the levels on Audio1, remove Audio1 or put my soundtrack everywhere. If I do anything to Audio1 Premiere mutes or removes all of the audio.....some of the time. In the current movie that I am making it is all of the time. If I do anything at all to Audio1 there is no audio at all.
I guess I'm not understanding what you're saying. Sorry. I have no idea how what you're describing is occuring.
It may be time to contact Adobe Tech Support so that they can walk you through some troubleshooting.