[xyzzy]

Just to be clear here I interpreted your original post as you created a rule (or rules) to test for certain domains and if matched to send those messages to spam and marked as read. In other words the checkboxes for the actual rule in the rules then actions were "mark as read" and "send to spam". It was that "Mark as read" checkbox I was referring to, not the Spam Protections "Mark spam as read".

So if you now checked Spam Protections "Mark spam as read" and it is "working" now that tells me those messages were (are) always being classed as spam and never using your rule(s).

I base that on the fact that clicking "Mark spam as read" in Spam Protections only adds the "read" flag where spam score is checked in the sieve code and that takes place before your rules are applied (determined by comparing the sieve code with and without that checkbox checked).

If you now have "Mark spam as read" in Spam Protections then all spam will be marked as read. If that's what you want, fine. But non-spam, i.e., messages that reach the rules would still need their rule's own "mark as read" as one of their actions.