If you are using a non-shopify theme which is custom then it may happen that CSS selector which app is using isn't reliable. App currently uses following selector so it's possible it either doesn't exists or located at very bottom of page.
#shopify-section-header
In that case, we recommend using another selector (generally header) which would make sure pop-up appears correctly.
1. Visit "Global Settings" tab once you open an app.
2. Scroll down and you would find "Unique CSS identifier" under "Advanced Settings".
3. Specify your unique identifier without "#" and hit save. Make sure your selector is present on all pages for app to function properly. We generally recommend selector from footer section.
Note: Selector needs to be an ID selector and not a class selector.