Most used files are disappearing

Hi all, not sure if this is the correct place to ask, otherwise pls tell
me where.

We are experiencing problems on a machine on Scientific Linux 3.3 which
has kernel 2.4.21 and ext3 : all the files in most used directories are
disappearing.

Usually the granularity is the directory: at a certain point one
directory is completely emptied. Usually this happens on one directory every a few days.

We have other machines with that distro/kernel but we are only
experiencing problems on that one.
We tried looking for bad sectors in the disk (with badblocks) but apparently there are none.
We even reinstalled everything once, but the problem is still happening.
We changed all the passwords after reinstallation, and the problem is
still happening. We don't think we have been hacked. Few programs are
running there and I don't think its their fault.

Before system reinstallation, the machine was destroying so badly that
even /dev/ lost practically all its files while I was logged. Actually a
few resisted (or more likely they were automatically regenerated somehow
after destruction), I don't remember which.

Do you have a clue?

Also: if badblocks reports zero bad sectors, can I be sure that it's really zero bad sectors or maybe the disk has already relocated some bad sectors to some special area transparently, unbeknownst of ext3, and that's why data loss occurs? Does this make sense? It's an IDE disk.

Thanks for any help.
.