Conflict w/ another plugin

The fault lies in the Simple Intranet Directory’s code and the method they use to register the post type then flush the rewrite rules.
They are including the flush_rewrite_rules() function inside the si_create_bio_post_type() function that creates the post type, which is run on the init action. Having it flush rewrite rules on the init action means it runs on every page load, which is not only horrible for performance, but also unnecessary and is likely what is causing post types previously registered to be wiped out.
Flushing the rewrite rules needs to be pulled out of that si_create_bio_post_type() function and instead moved into it’s own function that is only run on plugin activation. See: http://codex.wordpress.org/Function_Reference/register_post_type#Flushing_Rewrite_on_Activation