I have run into a similar problem occassionally,
does it do this consistantly ?
What does your "status of mail queue" log look like ?
if you see alot of email sitting in the queue?
also, what does your smtpfront-qmail log look like? does it show 2 entries for the double messages ?
As for the late delivery, there could be a few causes. I have had the qmail daemon die if there is a ton of email built up in the queue. watch the status of it during a busy day. Also, what kind of email volume are we talking about, and how beefy of a server for it ?
One of the things that I figured out that if they were using the webmail system (horde &imp) sometimes employees would click send on the message that they wrote, get impatient after like 5 seconds and click again before the window closed. my boss complained to me about double and triple emails.