Wordpress, Custom Taxonomies Broken Every Install - wordpress

I just created my first proper theme and I'm having trouble working out the last bug, I have a custom 'portfolio' post type with its own custom taxonomy (portfolio-category). However, every/any time I install the theme on a different install of wordpress (all latest 3.5) the taxonomie is broken, does not display where it is supposed to. This is after adding new 'portfolio categories' and saving.
Pastebin of my taxonomy code from functions.php and the code I call it in (for an isotope filter).
If anyone could help me I'll love them forever <3
Thanks!
Sorry, forgot pastebin link http://pastebin.com/eVqndBZP

You forgot the pastebin link but by past experience you probably just need to go to permalinks and press save.
Also see http://codex.wordpress.org/Rewrite_API/flush_rules

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