I can't recreate the issue here. I'm assuming you are doing more than just recreating the "M" command, since you could easily map that command to multiple keys if you wish (up to 3).
That said, I can't duplicate your issue. I create a macro with one command:
I open a new song file, add new tracks, and whatever track is active gets muted/unmuted as I select the macro.
Maybe I'm doing something different, but it's working for me.