Custom time signatures overruled by multirest
Start Musescore and use Untitled for this test. I'm assuming you get (as I do) a page of single empty bars with a time signature of 4/4.
Enter a note into bar 3 or later.
Right-click on the 4/4 time signature and select Time Signature Properties, enter 4 (or any valid value) into the left-hand text box and press OK. You will now have a time signature 4 (or the value you entered) and no denominator.
Press M. If everything looks OK, press it twice more. When I do this I see the multirest preceded by the original signature (4/4) not the intended one. It flips to and fro as you press M (the "twice more" only applies first time round).
Please note that this bug also applies to a custom time signature created by the Create Time Signature route, and also applies whether or not the custom one has a denominator.
This has happened to me