If Spam Detector is On and Spam Filtering is set to "Delete incoming spam", is the spam sent to the Trash folder?
I recently didn't receive several emails that were received by Verizon's mail servers (per my email fowarder's logs). I found that Spam Detector was on, though I'd turned it off years ago due to missing emails.
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Actually I meant if you chekd it it will go to special Spam Detector folder rather than trashing it immediately. But I would guess you already figured that out.