Deleted files

[Walls Rob W Contr 75 CS/SCBS]

Thought my troubles were fixed, but files disappeared again and reappeared
after a few dozen rsync cycles.
I am mapping a Win2K directory to Linux with Samba. That mounted directory
is then Rsynced to another Linux box on a schedule (Linux to Linux, because
I can't run rsync on the windows machine).
For some unknown reason, several thousand files are periodically (after
several days) deleted from the remote Linux box. Running Rsync a few dozen
times seems to get things back to normal, but causes great stress to myself
and my users.
I am using the delete option, but these files should not be deleted, because
they haven't changed. Files eventually get back in sync. I can't figure out
why they are deleted in the first place.
Any ideas on what to check? 

Rob Walls