1) My upgrade from 2.0.2 to 2.0.4 was completed by following the upgrade instructions exactly as written and this means that the functions-formatting.php file was indeed copied over to the server and replaced the old copy. I have since copied it over multiple times and restarted my web server and cleared my browser caches in the hopes of 'shaking something loose' but to no avail. Could this behavior be affected at all by MySQL and the way that table data is being retrieved?
2) By 'tag' I'm referring to a specific script function in a php doc.
3) Here is the code from my default-filters.php file. The specified line has not been commented out:
// Default filters for these functions
add_filter('comment_text', 'force_balance_tags', 25);
add_filter('comment_text', 'wpautop', 30);
add_filter('comment_text', 'convert_smilies', 20);
4) The link actually works if I use the full anchor format! But wow, that's a pain. When I finally publish the blog on the web I'd like people to be able to easily add clickable links to the comments without having to write html.
Thanks for your help. It's much appreciated.