comments are coming on improper posts in WordPress

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 work, do this:

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