Why doesnt windows file protection work right?

After using XP media edition 5.1 for several months without problems,
I now get the file protection pop-up and when I insert the XP disk it
loads. But after removing the installation disk, the message will
return at times.
I can click on "cancel" and "yes" to keep the unrecogonized files and
the box returns immediately.
I restored the drive image made very soon after installation and have
the same problem.
I also used msconfig to stop all programs from loading on start up
with no luck.
The only way I can keep the error box from returning is to keep the
installion disk in the CD all the time and it randomly loads.
Is there a utility that shows hard drive activity and logs every
file written to disk? If I knew which files XP was copying I might
be able to locate the program that is causing the problem.