Thank you for sharing your great forum plugin and quite frankly it beats the pants off of any other WordPress forums.
Saying that, there is a bug in your plugin that incorrectly flushes the rewrite rules and it breaks custom post type permalinks.
I've tested it again and again and it's your plugin. Commenting out this line below in your wpf.class.php does the trick, however the permalinks need to be re-saved for the friendly seo urls to work on the forum again.
//add_filter("init", array(&$this, "flush_wp_rewrite_rules"));
Just a heads up for your next release.