I checked "Mask Comments author's link". I unchecked and rechecked it and it still wasn't working, so it must be the theme I'm using.
I could rewrite .htaccess, I've done it before and added some of my own rewrite rules, but I don't want to download an older version of the plugin. Its not a big deal. I thought I could just change something in the wp-noexternallinks file. After looking through the code... can't I just change this line in function parse_noexternallinks:
$url=get_option('siteurl').$sep.$url;
To
$url=get_option('home').$sep.$url;
siteurl points to where the WordPress core files are, while home points to the main index file (for those that store WordPress in another directory). It seems to make sense to change it there, but if I change that should I change this line in function wp_noextrenallinks:
$site=get_option('siteurl');
Not sure what that does, but it seems like that is used for excluding internal links.