Custom Permalink Structure

I am currently using the blackfyre theme and have spent the last 3-4 hours troubleshooting why my permalink structure wasn’t being saved. For the longest time I thought it was a issue with my .hta file or the apache mod_rewrite not being enabled. After endless troubleshooting, my last steps (Which should of been my first) was to disable all plugins and try to save my custom permalink. That did not work. So I disabled the Blackfyre theme and enabled a default wordpress theme and the custom permalink structure saved, and corrected all my pages links.

Is there a fix so I can use “/%category%/%postname%/” as my custom permalink structure with your theme? Is there a reason why the theme isn’t allowing that custom structure?