At the risk of sounding foolish, I'll jump in with my
opinion. I' m no security expert either, but have learned
something about security.
I think your terminology for "rooted" is shall we say "creative".
The fact the all of your files were wiped from the disk, and
you seem to have ruled out hardware failure, the logical conclusion
is that some process/user with root-level authority deleted all the
files. The fact you discovered rootedoor after reinstalling doesn't
preclude the possibility that it *was not* there before. I don't
know the specifics of your machine and you certainly seem to know
what you are doing, and I'm not suggesting you wipe your machine.
I don't know if/why any of your clients have root level access, so
if they do then it is certainly possible that one of them did it by
accident, as you seem to think. I find it unlikely that some arbitrary
process did this, and if it did then you need to seriously look at the
uids that these processes run as. There is no reason for most programs and
I see no reason for any web program to run with root privileges. I am curious
though how the re-install was accomplished, seeing as how you live here in
the KC Metro and the machine is 1000+ miles away in AZ, IIRC.
I'd also like to say, that it appears by your numerous replies on this these
threads that you take pretty good care of security, which makes finding out
what might have happened more important. Since a successful hack might indicate
a zero-day exploit, while it could also be highly likely that a local user's
account has been compromised.
Brian