Outlook's Junk Mail filter is enabled, but you still find junk mail in your custom folders. Where does it come from? Well, truth be told, it comes from Hel...<sorry>.
Seriously, I have many rules that shuffle messages into recipient- and topic-specific custom folders. Occasionally, a junk message shows up, even though the junk mail filter is enabled. The explanation is the rule -- a rule that moves messages into a custom folder when it arrives.
You see, Outlook checks incoming mail against rules before running it by the junk mail filter. When mail arrives and it satisfies a rule, into the custom folder it goes -- even if the message would also qualify as junk mail. Outlook never even checks the message against the junk mail filter.
Unfortunately, this is just one of those behaviors you have to live with. You can try to rewrite your rules to reduce the amount of junk mail that makes it into a custom folder. Whether the work is worth the effort is debatable -- just depends on how much you hate that junk mail. Unless you're dealing with lots of it, it's probably easier to delete the occasional message that sneaks by.