In Linux, my Brother MFC-J480DW cuts off top margin when used with A4 paper, even if all settings are set to A4.
To make it work, I had to edit /opt/brother/Printers/mfcj480dw/inf/brmfcj480dwrc
file (that's the path in Gentoo, it could be different in other distributions).
And change:
PaperType=Letter
to
PaperType=A4