I dont have much experience with the outlook junk filter since I use a different software to get rid of junk, but, I remember that, if you do not enable cached mode, you cant customize the filter.
That sounds like not the server, but outlook does some of the filtering on the client. This only works if outlook is running.
From what you tell, it looks like just this is happening: The filtering of junk is handeld by outlook, and not by a server based rule. Any rules which are client only will be executed after the BES gets the Email. Eventually the automatic reconcile might then apply the changes which outlook did back to the blackberry. However, this does not work reliable.
To check this, stop using outlook for some time, and use outlook web-access instead to test the rules.
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