FYI below is the response I received from SM support. If this is correct this is a big change from how the system previously worked (7242 and prior). Previously emails would be processed by spam filtering and then content filtering without issues. I am opening a ticket for clarification and workarounds if needed.

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In SmarterMail spam filters will be the first filter a message is hits. Messages will only go through one content filter. So if a message is mark as spam by the spam filter it will not go through a domain or user content filter. I'm not sure how long the content filtering has worked this way, but it has been implemented like this for quite some time.

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Hi, Jason

Filters run in order: Spam filtering first, then content filters. Then, content filters run top-down in order.

That said, as long as your spam filter doesn't delete or move a message (to Deleted Items, for example) content filters SHOULD also run on messages after they've gone through spam checks.

Derek,

    Thanks. I have opened up a ticket for this, I do believe there is an issue right now with the spam filters and content filters working correctly. 

Yeah, I see it Jason. We'll do some testing on our end as well, just to make sure.

Good morning all. Sorry for the late update but this has indeed been found to be a bug. The ticket is still open and support will hopefully be getting it squished in the next week or two.