Tamper-Proof Atlas Passive not working

Just ran into a couple strongboxes that were blue and not rare.
Was fine before the latest update.
Also havent run into a single harbinger since the patch despite having the Ominous arrival passive and actively re running accross bits of the maps seeing if i missed one.

Have you been running Kirac missions? They do not count as being on the atlas so the atlas tree does not apply.