The problem was that theme_token_tree($variables) was being passed only a subset of available tokens. Just a gotcha to look out for if you haven't done work with the token tree before.
$variables = array('token_types' => array('nodes','comments'), 'global_types' => FALSE);
theme_token_tree($variables);
I needed to add additional token types to the token types array, like so:
$variables = array('token_types' => array('nodes','comments','bean'), 'global_types' => FALSE);
theme_token_tree($variables);
You can also go to /admin/help/token to get a list of all available tokens. Be warned though, unless you have enough memory allocated to MySQL it could consume all of it and give you a "MySQL gone away" error. I received that error and I upped mine to 500MB locally and it was fine after that.