This is easier said as done. mke2fs doesn't touch the devices boot sector.
This is required as mke2fs's job is not to think about booting. Actually
it might be required to not look there as some partition info might lurk
there. The bootsector is simply not part of a partition.
Now however MSDOS illegally place it's filesystem (well.. no I was already
(correctly) critized for my negative attitude, so I won't comment on DOS
FAT) info in that bootsector. So mounting something as (u)msdos has to rely
only on the bootsector.
I think I heard that at least newer versions of mke2fs allow to clear the
bootsector by use of a flag. Use that with care. It might destroy some vital
data.
What you describe is a general problem when making a new filesystem over
a dos formatted device. In that situation you might consider overwriting the
bootsector by hand b4 making the new fs. It has actually nothing todo
with e2fs. Other fs suffert from the same (DOS) problem. However usually
people experience it more with floppies.
Still umsdos might/should have detected that something is wrong coz it
would have been unabled to find some of his special files for the files
permissions.
Michael.
(eowmob@exp-math.uni-essen.de or eowmob@pollux.exp-math.uni-essen.de
Please do not use my vm or de0hrz1a accounts anymore. In case of real
problems reaching me try mat42b@aixrs1.hrz.uni-essen.de instead.)