When Pathagoras processes text and replaces variables, it is supposed to 'clean up' after itself, and return all view settings to the state they existed before you began. However, sometimes Pathagoras does not. A step errors out the program and it cannot recover. Other reasons may exist why Pathagoras did not earn the Good Housekeeping seal for that session.
The second tab (Settings & Views) allows you to set your preferred 'start up' and 'end up' settings for documents created with Pathagoras.
Tell tale signed of these issues is that you will see Microsoft/Word 'fields' and not their values. If you see a Table of Contents and Page Numbers with funky text (generally between light gray curly braces) you are viewing the 'field'. Pressing Alt-F9 with cure the issue, and show the values, but you would rather not have to do even that.
Here is where the 'Setting & Views' screen comes into play. Regardless of processing errors, Pathagoras will attempt one last time to restore you document to the preferred view as determined by this screen.
Select the preferred views and settings. Be sure to check the 'Always return document to these settings' box. Press Save to lock in your choices.