You /are/ running Windows Mail on Vista and not Outlook Express, correct?
Is this a pop3 account?
Turn off e-mail scanning in your anti-virus program. It is a redundant
layer of protection that eats up CPUs, slows down sending and receiving,
and causes a multitude of problems such as time-outs, account setting
changes and has even been responsible for loss of messages. Your
up-to-date A/V program will continue to protect you sufficiently. For
more, see: http://www.oehelp.com/OETips.aspx#3
Note that for some AV programs, it may be necessary to uninstall the
program and reinstall in Custom Mode and uncheck e-mail scanning when the
option arises.
Your email provider probably has a web access to your messages. If they
don't, then there are other web sites that provide the service for free. You
can check online to determine if there are multiple copies in your email
provider's server. If the multiple copies are there, then you know there is
nothing wrong with your system.