Thanks for your reply. I've tried the "User Role Editor" plugin and added the role "unfiltered_html" to my users but still no luck when posting <iframe> tags. Which WordPress version are you using?
I was only able to post <iframe> tags when editing wp-includes\kses.php similar to the description here http://www.kavdesign.net/blog/coding/how-to-disable-wordpress-html-filter-for-posts-and-pages/.
After commenting out the following lines:
// Comment filtering
if ( current_user_can( 'unfiltered_html' ) )
add_filter( 'pre_comment_content', 'wp_filter_post_kses' );
add_filter( 'pre_comment_content', 'wp_filter_kses' );
posting <iframe> tags was possible but I did not find any conflicts with the WP-Ajaxify-Comments plugin. I think your problems are not caused by my plugin. Please make sure that the <iframe> tags inside the comments are really saved in the database and are returned to the theme when rendering the comment section.
Hope this helps...