MySQL, Mail, and FTP would be one thing but am I correct in assuming
you are talking about Cpanel / WHM / SSH passwords?
For the later, the passwords are related to the server so it doesn't make
any sense that a changed password would still work unless an open session
were carried forward perhaps (See files in /tmp) or a new account were
created but then that would have a new login.
Does the user have duplicate entries in /etc/passwd?
(/etc/shadow .... same question)
Interserved may have made that side RAID comment thinking that perhaps
your user account files weren't getting updated but if that were the case
then the new passwords would not work and logins would only work with
the original unchanged passwords.
I don't know, it is is as you say, there is something definitely really screwy
going on with your server that does not make any logically sense without
seeing things and digging into it first hand.