By default, popups will NOT appear on the Thank You page.
(See section 3.c of the tutorial http://ambitionally.com/popupally/tutorials/thank-you-page-setup/)
Go to PopupAlly – Display Settings. Scroll down to the section ‘Thank you page after signing-up’, and uncheck the page.
If that helps, you can consider upgrading to PopupAlly Pro, which include a lot more templates and features. PopupAlly Pro also includes email support and we’ll be happy to help you out with any further questions you may have. We have a 30-day money back guarantee on the plugin, so feel free to take it for a risk-free try. If you don’t like it for any reason, just let us know and we will refund your purchase.