Hello,
What service provides your email?
If you're not sure, what is the domain name (everything to the right of the @) in your email address?
Have you tried increasing your incoming pop3 mail server timeout setting from 1 to 5 minutes?
There are a variety of reasons why your mail connections could be timing out including anti-virus of other security software on your computer taking to long to scan your email when you mail program is trying to download your email.
It could also be a problem where their is a mail forward or message rule, either in your mail program or your email service providers servers, that is causing you to not get most of your incoming email.
If the service provider is not able to hep further we started offering a
live support service where we can work with you over IM or phone and login to your computer to help you troubleshoot the issue.