Comment 8 for bug 187598

A solution finally!

I stumbled on this page via launchpad bug reports:
http://solutions.brother.com/linux/sol/printer/linux/printsetlpr.html

It appears the CUPS settings do not apply with Brother's own LPR driver so you have to use their special utility to set the paper size correctly.

I logged in as root using sudo -s and then entered the following command:

brprintconf_dcp135c -pt A4

This fixed print alignment for me (using Brother official drivers).