I found the problem, it <i>was</i> SK2.
I had Spam Karma 2.0 Final r2 installed. While it was activated, the database isn't updated properly, specifically wp_posts in the comment_count category.
The fix seems to be to make sure that you are using Spam Karma version: 2.2 r3.
once you have installed the new version, future comments will be OK, <b>but posts with old comments need to be fixed</b>. There are two ways I know of doing this.
1) go into the database and do it by hand (yes, that's slow and you do need to know how to stumble around in mySQLadmin
2) go to every post that has the wrong comment count, and add a comment. When the new SK2 approves it, the total proper count will be corrected. You could then erase that comment, count should then decrement OK.
yea, both of those options suck. Sorry, that's the best I can do. Oh and I really wish that Dr. Dave would splash this all over his home page. I have months of posts that I now need to fix by hand.
threads that helped: