I am using Windows Live Mail. It retrieves mail for 4 accounts. It worked correctly for about 6 months. Recently I noticed that for one account, it is collecting only some of the mail, and leaving the rest of the mail for that account on the server. I can only view it by web mail.
I spoke with a tech at my server. We moved all the messages in this account to a temp folder, deleted the account, then reestablished the account, with all the appropriate settings, and it now worked correctly. We then moved the messages in the temp folder back into the correct inbox. Hope this helps if anyone else has this problem.