has the billion second bug patch been applied (on or since Sep 10) ? it's very easy to do, follow instructions on the e-smith.org site.
if you have vacation enabled (an add-on), try disabling it (one user to test).
if you know how to check the .qmail files, see if mail is directed to other than just Maildir (i.e. more than just a line with Maildir in it, comments not included), and if so try commenting out those other lines. I believe that if the any one of the .qmail file transactions fail, the file 'runs' again which can lead to duplicate emails.
reindex your email client(s).