Great plugin but one issue witch shortcodes

I have been playing with this plugin all this morning, set all the woocommerce emails but I ran into a following weird problem. I have also automatewoo installed which sends email for a specific product trigger. Now, I created a template for that trigger and when I do a preview and send a test email from yaymail shortcodes show up fine, however, when I do an actual purchase, I get an email based on yaymail template but shortcodes are missing.