Poking around looking for an answer to your issue I found a few things that may help since there is multiple reasons this could be happening. Here is what I have found.
You may try these:
A) Try scanning the computer using Antivirus software because this issue can occur if the computer is infected with virus. You can do a PC Safety scan by clicking on the link http://onecare.live.com/site/en-us/default.htm and Clicking on the Full Service scan and accept the Agreement.
B) This issue might also be because the User Profile is corrupted, so create a new profile if the above step does not resolve. Then configure Windows Mail and check if its working.
1. Open User Accounts by clicking the Start button, clicking Control Panel, clicking User Accounts and Family Safety, and then clicking User Accounts.
2. Click Manage another account. If you are prompted for an administrator password ***** confirmation, type the password ***** provide confirmation.
3. Click Create a new account.
4. Type the name you want to give the user account, click an account type, and then click Create Account.
“Setting up Windows Mail “http://windows.microsoft.com/en-AU/windows-vista/Getting-started-with-e-mail#section_2
Check the link “Create a user account” http://windowshelp.microsoft.com/Windows/en-US/Help/68a1c4fd-b3f6-4cb9-93a1-8a6023836e531033.mspx#E1D
C) To recover the lost emails try these:
For Windows Mail, by default, the data is stored in the location C:\Users\<user account>\AppData\Local\Microsoft\Windows Mail
Check if the data is present in that folder. If it is present you can import the data to the Windows mail.
i. Open Windows Mail by clicking the Start button , clicking All Programs, and then clicking Windows Mail.
ii. Click the File menu, point to Import, and then click Messages.
iii. Click Windows mail, and then click Next.
iv. Make sure Import mail from a windows mail store directory is selected, and then click OK.
v. Click Browse, find the windows mail folder(C:\Users\<user account>\AppData\Local\Microsoft\Windows Mail) you copied to this computer, and then click the folder once to select it. (Do not open the folder when you select it.)
vi. Click Select Folder, and then click Next.
vii. Click All folders to import all the folders, or click Selected folders and select which message folders you want to import, and then click Next.
viii. Click Finish.
I would save option B for last as I'm sure starting from scratch is the last thing you want to try. :)