I was having a lot of issues with my custom taxonomy archive pages giving me a 404 when this plugin was activated, so I wanted to post my solution. If you remove the following line of code from the custom-post-type-permalinks.php file, and save your permalinks in the WP admin, it may fix your issue:
REMOVE THIS LINE (Line 161):
$wp_rewrite->add_rewrite_tag( "%$taxonomy%", '(.+?)', "$taxonomy=portfolio_category" );
Hope this helps anyone who may be having the same issues I was having!