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.)