I'm sorry to hear about the problem you're having. Have you worked through the Troubleshooting Guide and FAQs?
In almost 100% of cases where this is reported, there is something in the site that is interfering with the plugin's ability to function at all, so it's not just indiscriminately blocking comments...it's being prevented form functioning. This is usually due to a plugin conflict or permissions error on the server, and in almost every single case I've seen, the issue is more universal and affects other plugins and scripts that are installed on the site (sooner or later).
Once you have worked through the Troubleshooting Guide, FAQ's and check the known conflicts, the next step is to submit a support request so we can look into your issue, review the specifics, and help you fix it.
Once you submit a support request, if it turns out the plugin does need any kind of fix, I'll get on that right away.
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