I discovered that trying to mux elementary streams results in the dialog ignoring the Favorites Only check box. Even if I set it and then do another muxing run, the box is still unchecked.
So it's not remembering. That could be the case. Those dialogs are completely separate so they have different options. I could have forgot to remember that in ES, and since it's used so infrequently by users you're the first to notice.