Thank you for writing in and regretfully the portfolio filters are not supported when using a custom header. If you need filtering, you can use the bundled Essential Grid or the Grid plugin to power your portfolio page.
[x_portfolio_filters] as a shortcode. People can add it to a content area element and it will output the filters on a portfolio page. It will still use stack styling and may require some custom CSS to get it looking just right depending on how people end up placing it in the bar. This is more of a stopgap solution until we make a new blog/portfolio system later on.
Thank you for understanding,