Setting permalinks programatically breaks custom post type URL's

[gilbitron]

Using a function to programatically set permalinks (see attached) breaks custom post type URL's. A 404 page is displayed instead.

Visiting the Permalinks settings page fixes the issue (you don't even need to save the permalinks settings).

It turns out that you need to call $wp_rewrite->flush_rules() on the following page load for it to work, even though this is called at the end of the modify_permalinks() function.

Possibly related to #16736

[scribu]

It's important when you're calling modify_permalinks() as well.

[nerx]

Just to mention: $permalink_structure will collapse if you use it to modify!

[nacin]

I could see this being an issue if the post type isn't registered before modify_permalinks() is called. So, wait until wp_loaded.