Your need to listen to what I said 🙂
The plugin may behave differently with different theme, because it depends what happens during the loading of the page.
If when the plugin computes the position, the theme has already loaded everything, it will be fine, but if the theme still does some things after that, the position will be wrong.
It is the job of the plugin to make sure that they compute the position AFTER everything is loaded, if not the result may be wrong.
So this is NOT a theme issue, but a plugin issue, and you need to speak with the plugin developer.