I am having the custom template / pagination issue as well. I just updated the plugin, but the pagination still does not work. I just posted this as a question here: http://wordpress.org/support/topic/pagination-not-working-42
sorry for the duplication, however it does not seem resolved for me. thanks!
I’m having this problem too. It looks like you fixed it though? Are you still using a shortcode?
Great! Thank you so much!!