Hello,

The portfolio categories will show the portfolio items of that category for only the items already displayed in the present page. Not the items from other pages.
Please refer to this topic, to display more than 9 items per 3 columns. In you case, you should edit only this part:

case '3':
  $p_per_page = 9;
  break;

To this:

case '3':
  $p_per_page = 999;
  break;

Best regards!