It this only a screen display issue? - or do the rectangles print?

To check whether the rectangles print, export as a PDF file, and examine the PDF (= no need to waste print paper).

… certain noteheads are randomly becoming rectangles …

If I understand your word ‘randomly’ correctly, the same pitch may sometimes display a regular notehead, and sometimes a rectangle - right?

Are all the rectangular notes notes with ledger lines? Could the problem be a too-thick ledger line setting?