How does MM identify blank pages? I have a book where every chapter starts on a recto page, requiring that sometimes the preceding page be blank. Among others, I have an A Master (with header and footer) and a Blank Master (which is based on None). The chapter number paragraph style is set (in Keep Options) to start on an odd page. The author keeps revising the text which sometimes requires the addition of a blank page, but MM leaves these as the A Master (with header and footer) whereas in the MM dialog I specify that the Blank Master is to be applied to blank pages.
A page which has nothing on it, or only empty text frames, is identified as a blank by Mastermatic.*
If a page is blank because of a “keep” option, that is also identified as a blank.
So there is no reason that Mastermatic shouldn’t work correctly with the setup you describe.
What about object styles? Perhaps you’ve got an object style that is causing Mastermatic to apply a master page (under the Object tab in Mastermatic)?
A screenshot of your Mastermatic settings might help.
(* The only known bug/limitation is in the case of continued tables or continued footnotes. If a text frame contains only the continued part of a table or the continued part of a footnote, it is incorrectly identified as blank.)