There was some point along the OS line where Macs with built-in floppies lost the ability to write and then read 400k MFS floppies.  They kept working with 800k until the bitter end, though.  I just ran into that tonight... my Quadra running OS9 wasn't able to read a 400k disk; it wanted to format it.  But popping it in an earlier machine running 7.5 read it fine.

This is a decent treatment of the subject:

http://siber-sonic.com/mac/newmillfloppy.html