Some good news at least. I have not surveyed all twenty-odd-thousand to see if their boxes are checked. It appears to be a healthy mix of checked and unchecked as I cruise through quickly.
As for your initial grout of questions:
I am using Apple Mail. I mark a message as spam by selecting it and striking control-command-S.
I have no other active rules in my Apple Mail rules list, just “Spamsieve.”
I am only using Spamsieve on my desktop rMBP, and no other computers.
I rarely delete spam from my phone, and never did until the last few weeks when I have been getting perhaps a hundred or more spams a day in my inbox. I did not know that was a problems, but still have not done it much, though I m sure much more than you like. When one is away from his desk, and one gets many spams per hour, it becomes difficult to keep track of one’s email.
Yes, it appears as if the statistics are moving along with my marking of a spam message.
Turning off auto-training: frankly, I don’t know enough about it to know if this would be a good idea or not.
So, in review, I seem to be doing not much wrong except deleting spam from my phone (my accounts are all IMAP, by the way, including the one via which 99.5% of my spam arrives) and you seem to be saying that I should reset the corpus.
Any other immediate questions or tips, or should I just reset the corpus without doing anything with the other files?