comments are coming on improper posts

It sounds to me like you mucked up the query and the comment form thinks the user’s on the wrong post. Try adding

wp_reset_query();

to your theme right before your theme adds the comment form.

If that doesn’t work, do this:

wp_reset_query();
global $post, wp_query;
$post = $wp_query->post;
setup_postdata($post);