Sorry I should have mentioned this. Since I upgraded to Office 2010 and Windows 7, I've had an IMAP account which apparently is why I can view all my folders on the server (not the Outlook Data File folders which I barely understand the meaning of). As mentioned, I can see the missing folders there.
I've just run the Inbox Repair Tool as in Ken's reply but to no avail. (I did the 'fix it for me' method.)