Duplicate mails issue

Hi, at work i'm running a 1.8GHz Macbook air. Its main role is accessing mail from an Exchange 2003 server through the mail application. Recently a fault was noted where accessing messages took to long. The account was deleted from the mail application and set up a fresh. This took a full day considering the size of the mailbox(24Gb) and did not solve the problem. Next step was accessing the mail using a different time capsule but the same fault was noted. Apple technical support recommended a clean install of Snow Leopard(upgrading from Leopard) as a last option. This had the effect of mails appearing as duplicates, new as well as old backups in addition to not solving the old fault. The problem is not server side as the user still has access to his mail through his iphone and in addition a similar spec Macbook air with the same configurations and a larger mailbox(30Gb) does not have the same problems. The duplicating mails were noted in mail.app and Mozilla Thunderbird and Apple support insist the machine is not at fault.

Has anyone experienced anything similar and/or could suggest a fix?

I am experiences similar problems with duplicates (which can't be deleted). I can send mail. The activity bar shows messages being downloaded but they do not show up. The only way I can get mail is to get it into mobile me and then sync but the duplicates remain. I have deleted my mail account and set it up again with no improvement.