I may have a similar issue, though it could be related to the Ajax plugin (WP Ajaxify Comments) you recommend. One good Captcha plugin, Conditional CAPTCHA, claims here that Ajax-enabled comments aren’t supported. (Actually, I’m not yet convinced that Ajax-enabled comments are superior, given the issues noted here that would go away with page refresh.)
Ajax is still causing conflicts between plugins and themes. I plan to solve that with a completely reworked version of Inline Comments. But for now, I can only recommend to test other captcha plugins.
Thanks much, Kevin, and do keep in touch on revisions. For now, I’m simply not using AJAX, and things are fine.
Jim