for other users: I contacted the PopUp Plugin authors already. Here is the post: https://wordpress.org/support/topic/jetpack_subscription_form?replies=1
the proposed solution on http://webcircles.ca/2013/09/01/how-to-modify-the-jetpack-email-subscription-settings-when-using-a-shortcode/ does not seem to work anymore.
the shortcodes will show the input section and the buttons correctly. But I am not getting any emails.
you might check it here: http://www.digital-geography.com
thanks for your help. exactly resolved my problem!!!
sorry, forgot the link:
www1.digital-geography.com