Although this has nothing to do with your plugin one inherent problem with WordPress to this day still is the issue of sites making use of DKIM for sending out mail (servers may automatically include it). When the signature isnt properly put into outgoing email the recipient (who potentially verifies against it) will either not receive the signature or an imporperly made one.
The way to resolve this is quite simple and involves adding a few lines in their plugable.php file. This file incidentally is what plugins like Mail on Update uses when sending out email. More specifically it uses wp_mail() function. The problem with this function is that needs the following two lines before DKIM can work properly:
$phpmailer->Sender = $phpmailer->From;
Without it plugins like "Mail on Update" will not work (you don't receive emails). I have resorted to duplicating the wp_mail() function and placing it inside this plugin (since wp_mail() can naturally be overrriden by plugins) and have added the missing lines. This has fixed my problem and incidentally has also fixed all my other plugins who were using wp_mail() too. Yay!
So although this has nothing to do with this plugin i decided to point this out and maybe ask if this could be included so those who make use of such spam fighting techniques can also benefit. By for the long term it seems more a WordPress flaw. I originally opened a bug on this well over a year ago (see WordPress Trac #22837) and only recently has the problem been taken seriously and elevated to Major Bug. So maybe WordPress will finally fix it or maybe you or another plugin will just add the fix in officially and be done with it.