If the option is selected inside the accounts properties on the desktop machine cleaning the messages off the server – then the messages will be downloaded to the desktop and not available via outlook web access.
To fix this:
1. Open Outlook 2000
2. Click Tools in the file menu and select Accounts
3. Click the Mail Tab and click once on the Expedient Email Account in the account window to highlight it, then click the Properties button.
4. In the Account Properties, click the Advanced Tab
5. Remove the check from “Leave a copy of messages on server”
6. Click OK and OK. Click the Close button on the Accounts window
Message will need to be deleted from the hand held for them to be permanently deleted.
it could be also that you are choosing to download you enail to your personal folder , from out look choose to view the mailbox