I completed my first run on the Normal Diff of the game, I collected every possible item and was bugged with the "Dr. Croft" locked cheevo, after the patch to fix it I loaded, reloaded the game and the extra "steps" and finally got the completion registered at 100%. Then loaded it and started my NG+ on Deadly Obsession, upon completion I had only 2 achievements left to unlock:

One with the Jungle
Complete Shadow of the Tomb Raider on One with the Jungle difficulty

Deadly Obsession
Complete Shadow of the Tomb Raider on Deadly Obsession difficulty

None of those two unlocked after completing the game. Worth noting I disabled Steam Overlay during the final fight, and skipped the credits. Verified game files and everything, gonna try reverting to the beta and completing the final boss again but I think is bugged to the core.

If you have any ideas or insights share them with me. Thanks