I see a Stack Exchange participant who perceives unfair treatment, and is wondering if things are working differently in practice from how things are supposed to work. Also, this participant is confused about some moderator actions.
I have a suggestion for you, @MichaelHardy. If you haven't yet tried this, hit the "contact us" button in the footer. Write as calm a letter as you can (mainly so you don't upset yourself further), and include links and quotes so that someone who is just coming into the story can follow what you're saying. You can include specific questions about things you haven't understood, and you can include specific complaints and suggestions.
I am a pretty recent arrival at SE, so I can't guarantee that this will be helpful, but I do think it's worth a try.
By the way, please do experiment with flagging comments. Here is a page that talks about comment flags: http://meta.stackexchange.com/questions/17364/how-does-comment-voting-and-flagging-work I am a little confused about what that page says about downvoting comments. Maybe that part is obsolete. But what it says about flagging comments matches my experience.