Actually, just worked it out. Put this in your functions.php file:
function prefix_reset_metabox_positions(){
delete_user_meta( 1, 'meta-box-order_post' );
delete_user_meta( 1, 'meta-box-order_page' );
delete_user_meta( 1, 'meta-box-order_custom_post_type' );
}
add_action( 'admin_init', 'prefix_reset_metabox_positions' );