Hey @rasso et al., I know this is several years old now, but I just had this problem, and this thread helped me solve it.
But.
There was one thing missing that I had to learn the hard way.
meta-box-order_custom_post_type
…should be…
meta-box-order_[YOUR custom_post_type SLUG HERE]
So, in my case…
meta-box-order_communities
When we add in @tdmalone’s helpful addition, the full code becomes…
function prefix_reset_metabox_positions(){
delete_user_meta( wp_get_current_user()->ID, 'meta-box-order_post' );
delete_user_meta( wp_get_current_user()->ID, 'meta-box-order_page' );
delete_user_meta( wp_get_current_user()->ID, 'meta-box-order_YOUR_CPT_SLUG' );
}
add_action( 'admin_init', 'prefix_reset_metabox_positions' );
