Progressive Beherit in vanilla dissonance location doesn't progress counter

[SoulSoldier64]

2.2.4
Picking up Progressive Beherit from a vanilla dissonance check doesn't progress the counter. (haven't encountered other progressive items yet) Had Dissonance 5, picked up progressive Beherit from Nibiru and was given dissonance 5 again and cannot complete game.

https://www.twitch.tv/videos/1817501528
40:45-40:55
Tracker shows dissonance 5 and doesn't change.

I'm had trouble getting the exact situation reproduce on my og file since I accidently auto-saved before I realized, but I confirmed this using a speedrun practice seed from this doc bellow - part2 4 before nibiru. It has all 12 skulls and the dissonance chest openable. Currently has level 0 beherit, but picking it up you receive level 0 beherit. (Nibiru entrance is Yggdrasil bottom left ladder)
https://docs.google.com/document/d/1ATJbG8ttr8gAKVPR43gHTxVePvbO74Yd4EucnbR3Ibw/edit

(don't need to download anything, just showing how I reproduced it without hex editing my save)

Seed: 1163021851
Settings String: 0002300FFC0009750050644A2E040555