very large filecount filesystems

[Vectorz Sigma]

I have a mail server that has a very large number of files on its fs.  We're
talking in the 10's of millions of files.   Therefore, as you can imagine,
the differential comparison calculations nightly take a very long time and
even after extending the timeout period to something crazy like 6 hours it
still times out.   Anyone have any performance suggestions for doing daily
differential calculations?