If the setting 'scan all pages for popup links' is enabled, the provided example No 15 'Login and reload entire page' from the Popups Test module does not display validation errors when the form is submitted with errors. Instead the page is just reloaded. This probably also happens with all other forms.

The error occurs, because the json for the popup returned from the server includes popups settings (js.setting.popups), which are different from the already present popups settings. The function Popups.addJS (~line 701) from popups.js takes the newly loaded settings and overwrites the old ones, thus breaking popups functionality.

To correct this, include the following at the end of Popups.addJS in the file popups.js.

Before:

       }
      }
    }
  }
  // Add new JS settings to the page, needed for #ahah properties to work.
  $.extend(true, Drupal.settings, js.setting);

  return inlines;
};

changed to: 

        }
      }
    }
  }
  // Exclude newly loaded popups settings, because this breaks functionality
  if (typeof(js.setting.popups) !== 'undefined') {
    delete js.setting.popups;
  }
  // Add new JS settings to the page, needed for #ahah properties to work.
  $.extend(true, Drupal.settings, js.setting);

  return inlines;
};