I am new to this community. I have similar problem but it happens with the e mail I compose, not what is in the inbox.
In my trash I see several copies of my email that I composed. Could this be because while I am typing, Mail saves everything automatically every few minutes ? How can I stop this ? How do all these end up inTrash ?
I am using Mt Lion
My symptoms are as Zeaman. It seems that if I REPLY to an email a copy gets created every minute until I complete the mail. I started to reply to a mail but got interupted . In the end the reply took about 22 mins to create by which time I had 22 copies made somehow.
I note reports of this problem going back to 2009. How can something like this persist for 5 years without being fixed?
I was having the same problem with multiple emails being generated to two separate POP accounts. After cheking with our ISP to confirm that the problem was not at their end, I tried Ernie's solution below and so far it appears to have worked. I did copy the old MessageUidsAlreadyDownloaded3 file to a backup location before deleting it. Let's hope that this has solved the problem!