1. Get a faster Internet connection
2. Format your PC and install latest Outlook
3. Disable email scanner

In the past, we have done many test and confirm that the problem less happen in:

1. Freshly installed PC
2. Without email scanner
3. Outlook Express (occur more in Outlook)
4. Well-configured mail server

I hate to say this but HUMAN ERROR can be one

Go through each setting on every email users. Make sure they have configure Leave a Copy option correctly.

FINALLY:

Use Conversion View in your Ouklook and Outlook Express. It shows messages in thread, to make finding and removing duplicate email easier.

Good luck

Talk to me, pin@1.com.my if you need more assistance.