I am on 10.10.3, and this was also occurring on 10.10.2.
I am running Airmail 2 Beta, but went to Airmail 2 stable to make sure it was not an issue.
I have used SS for a long time successfully, but in the last month or so, it just stops working, and junk gets through. I can even select and train as spam and airmail moves them, but the stats counter doesn’t change on spam sieve and the log is empty, there are no Train (manuals) in there.
So I did a complete uninstall of SS and all of its files. I reinstalled SS and did the training. When I did the training, I saw the stats go up and it went into log, then a few hours later, the same thing, it becomes useless.
For the record, I have licensed 3 copies of SS, for myself, my son on airmail and my wife on mailemate. They are not having this issue. My son is using the same version of airmail as I.