You can check via webmail to see which emails don't match up with those on your email client.
It maybe the case that some of the email is corrupt hence why it will not import it to the email client in question. You may need to delete this email from the server (webmail) to stop this message from coming back up.
If this doesn't help could you post back to us but include a bit more information around the client you're using and what you doing on the client when this message occurs.
I get the message when I am managing my email account directly in Virginmedia on the web. What I am doing is moving some unwanted emails form my in box to Spam. Usually I do this once per week. In future I will do one at a time and see if it happens with a particular email.