Hi, sorry it's taken me so long to test this.
First, let me say that I've noticed nothing unusual on my site as far as someone hacking it with the exception of the comments problem.
I just did the following to test this plugin on my site and to try to get to the bottom of the problem I had with it.
I opened the Disable Comments plugin's settings page and checked that all the options were still ticked. Yes. I took a screen shot of that page.
I checked that the Disable Comments plugin was active. Yes.
I opened the single loop page in my child theme of the Twenty Ten theme and restored the comments code line, which I deleted when I originally noticed that the Disable Comments plugin appeared not to be working since I had comments everywhere.
With that line restored, I checked one of the posts that I knew had been bombarded with more than 500 comments. All the comments were back.
I put my site into maintenance mode with WP Maintenance Mode, which is a new plugin that I just added to this site in the last couple of weeks. It was not on there when the comments stuff was originally hacked.
I deactivated every other plugin on my site. With each deactivation, I checked if the comments on that post were still there. Yes, they were. With all plugins turned off, the comments were all there.
I took a screen shot of the comments.
I have reversed everything now because I don't want that stuff on my site.
And I will send you the screenshots if you want them.
I don't know what to tell you. I certainly understand you defending your plugin, and I'm sure you know it backward and forward. All I can tell you is there are comments showing up on my site unless I delete the comments line in the loop-single file manually.
I'd like to get rid of the hacked comments, but I don't know where they are sitting in my database.
I'll keep them for a little while anyway in case you want me to test something else.
Thanks for addressing the problem. Sorry I don't have better news or better insight into what went wrong.