When I open up Outlook it says its 'downloading message 1 of 3' but when 'send and recieive' has finished there is often only 1 email in my inbox.

Can anyone explain the mystery of the vanishing emails?

It's possible that 2 messages failed to download and are still on the server, you'd be seeing the same thing every time you clicked "send and receive".

Check your settings - there's an option not to download messages over a certain size.

Do you have a spam folder to which these mails get sent?

If possible go to your email providers website and log in there, then you can see all your messages and find the trouble-causing blighters! :)