id	summary	reporter	owner	description	type	status	priority	milestone	component	version	severity	resolution	keywords	cc
16786	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"	defect (bug)	closed	normal		Rewrite Rules	3.1	minor	worksforme	2nd-opinion reporter-feedback