I’ve checked into things, and without actually having access to a PremiumPress theme, I can’t diagnose what’s going on. I did search their forums, and it looks like custom post types are usable with PremiumPress themes, and they use the standard method (that I’m using) to create custom post types. The only conclusion I can come to is the theme you’re using (of whatever system they use for their stuff) is interfering – and it’s a bug with them. (I see they have a plugin available to their members – custom post type permalinks?)
You can open a support question with PremiumPress to see what’s going on, and if they’re willing to discuss it with me to help find a solution, you can pass along my email address: brass.blogs AT gmail.com and they can contact me directly. But from what I’ve found, it’s not an issue with my plugin – it’s an issue with their themes. (I can say with certainty that I’ve used this plugin on a myriad of different themes with no issues at all.) Without having access to whatever theme you’re using, I can’t come to any other conclusion (and I’m not dropping $599 on stuff I’ll never use, just to see what the issue could be).