Can you show us screenshots of what you are trying to achieve? It's a little difficult to know what to suggest until we see more information.
You don't tell how you did set up the 'checkboxes'? Are you using the Checkboxes Learning Interaction? That is a static interaction, which means it doesn't have an automatically inserted Pausing point. You need to pause the slide manually by insertion of an interactive object like a button. That button can then be used to check if all checkboxes have been checked off, using an advanced action. Can provide more help, but you first have to answer the question about the set up.