In all of my adventures yesterday in reworking the permalinks I ran into some caching issues. It took me a while to figure out that it was a caching issue. Anyway, I came across this article which tells how to flush the WP rewrite rules.

/* I've lied to you, there are 2 solutions */

/* A function: */
flush_rewrite_rules();

// And a method of the global object $wp_rewrite
global $wp_rewrite;
$wp_rewrite->flush_rules();