permissions changing without notice

I have this very strange problem and I hoped all you knowledgable techs might
have an answer.
Some background: late last year one of my customers had data corruption on
one of their computers. I restored the corrupted data from a backup but
noted there were disk errors on the main hard drive in Event Viewer. I
suggested replacing the computer which the customer did. I installed all the
user data and setup the computer. But the new computer started getting disk
errors also. I finally traced the problem to a bad external backup drive
that was causing data corruption on the main HD only, and only when Windows
Backup started. I removed the bad external drive and the disk errors
stopped.
My problem is that since then sometimes on some files and folders
seemingly without warning, their access permissions will change. Even after
explicitly setting the permissions on the folders some of the files in those
folders will become inaccessable unless I use the local admin account to take
ownership and then re-add the permissions manually. I have reset the
permissions at the folderlevel but not all the files in the folder change
their permissions. I have to change the permissions on each file manually.
The computer is running Windows XP Pro. Let me know if you need more
information.

Thanks in advance.

John