Junk Email filtering in Outlook only works when there is a default PST or OST data file, and then it works only on email delivered to the Inbox. Therefore, if you have a server rule that moves mail to other folders, spam will not be filtered. Instead, have rules that move messages be client-based by including the condition, "On this machine only". That way, Outlook's Junk Email filtering will be active before rules to move messages from the default Inbox take effect.
In addition (or alternatively), you can enable server-based Junk Email filtering within Options of Outlook Web Access.
