I have magellian2 version 5.81 on my Peg1
I've got two hardrives one of which has 2 partitions which are about 4 gigs each. I've never had a problem reading and writing to them. I've used this on my "real" amigas as well, of course.
my Amiga 2000 used OS3.9 and of course MOS is really based on 3.1 or something like that, but it still works just fine.
there's got to be something else wrong with your setup.