If a blogger sets a static page as the WordPress home page (Options->Reading), the Subscribe to Comments plugin subscription manager will not work.
Here are the steps I took to fix the issue:
In the 'Subscribe to Comments' admin panel, find the options for Subscribed and Entry Author.
For Subscribed, enter this:
You are subscribed to this entry. <a href="[manager_link]&page=index.php">Manage your subscriptions</a>.
For Entry Author, enter this:
You are the author of this entry. <a href="[manager_link]&page=index.php">Manage subscriptions</a>.
You also need to find all the text in subscribe-to-comments.php that says 'wp-subscription-manager' and also add in '&page=index.php'.
You need to find the function 'manage_link' and add:
$link = str_replace('%2540', '@', $link);
around line 762 before the if statements.