Junk mail filtering does not work by design when Outlook is not running in cached exchange mode. To turn on cached exchange mode:
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On the Tools menu, click E-Mail Accounts, click View or change existing e-mail accounts, and then click Next.
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In the Outlook processes e-mail for these accounts in the following order list, click the Exchange Server e-mail account, and then click Change.
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Under Microsoft Exchange Server, select the Use Cached Exchange Mode check box.
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Exit and restart Microsoft Outlook.
For more information, see:
http://office.microsoft.com/en-us/outlook/HP010223431033.aspx