I had something similar (and still have on one maillist).

In my case: from server A (a gmail account) I had a filter to copy the mail to pop3 server address - so there were (always) two copies: a) gmail where it was originally sent, and b) the local pop3 server.

When I started using the local server as imap rather than pop3 I noticed that some maillists I subscribe to have double entries (not all mail, as you say) - but that seems to be coming from the maillist server.

I need to research what I have done - how I am registered with the email server - but I do recall I was 'playing' with a "copy" setting and I may have inadvertently set it up to send two copies.

In short - make sure you do not have any filters active that are copying incoming emails.

Remember the (imho) key difference between imap and pop3 is that while imap may copy a copy to the client the "real" email is on the server, while pop3 copies an email from the server to the client, then (by default) deletes it from the server inbox.

In short, verify your settings.

Hope this helps you (search for a solution).

Thank you aixtools

I remember I have got an active copy filter, I had forgotten the original mail app existed, all I have I have to do now is find the copy copy function and cancel it. A magician I am not, but you have given me the direction to head in, much appreciated.