Mail doesn't appear in Inbox, MBA OS X Yosemite

I have recently purchased a new Macbook Air (Early 2014)
Whilst trying to set up my hotmail account on mail I have encountered a slight problem. All of the messages that I have in folders in this account such as Flagged and Trash etc appear but my inbox remains empty. Any ideas on how I could fix this would be extremely useful!

Try rebuilding the mailbox. This can take awhile if you have a lot of mail.
Rebuild mailbox

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    This problem can be easily reproduced if you have more than one email account configured in iOS 4.x
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    Message was edited by: Ichinisan
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    Message was edited by: Ichinisan
    Message was edited by: Ichinisan

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