I left a test comment link using HTML on your blog at http://truenorthalliance.com/blog/bonsai-learning/, and the HTML was disabled properly by the plugin.
The plugin does not block comments with HTML, it simply disables the HTML from working when a comment is viewed. For example, when you tested the link in a comment you may have noticed you can't click it like a link, because it is rendered as plain text, exactly as the tooltip bubble explains next to the option. Hold your mouse over the question mark, and you'll see the explanation.
There is no reason to block a legitimate comment that uses HTML, when the plugin will render the HTML useless while allowing the comment through.
The checkboxes not remaining checked isn't something I've seen, nor has it been reported by anyone else. The checkboxes are rendered using the Settings API which I have not direct control over. It sounds like saving the checked box works the second time, so at least it's a quirk that isn't fatal.
I got your messages on toddlahman.com, and saw that you tried to reset your password. I added a login box, and a link to reset your password on toddlahman.com, to make it easier to use the support forum if you log out, or forget your password. Knowing you were having these issues are the reason I replied here, rather than referring you to http://www.toddlahman.com/forums/forum/spam-free-wordpress/
Check your Junk E-Mail or Spam folder for your password reset.
To summarize, the plugin is working exactly as it was designed.
I hope you will give the plugin a better rating than 1 now that you understand how it is working.