populate_network() doesn't set up rewrite rules properly
|Reported by:||duck_||Owned by:||duck_|
The call to flush_rewrite_rules() in populate_network() doesn't actually do much because although the lines before update the permalink_structure this doesn't actually change the value cached in the WP_Rewrite property.
This means that incorrect rewrite rules are stored for the main site when setting up a network. NB: this only occurs when the permalink structure had already been set to something before installing the network.
The fix would be to use $wp_rewrite->set_permalink_structure which updates the option and re-initializes the $wp_rewrite global to use the new structure.