It's working fine for me. Nothing involving crafting accuracy has been touched since Rep's last update.
If you truly don't have any mods altering the game's data, and are on the most recent patch, then I have no clue. Join Wofsauge's discord and maybe a cause could be figured out by you sharing your screen or such.
Also any BoC accuracy complaints should include the run's seed or else they're 0% reproducible.

This happens to me as well, especially in Greed/Greedier

I tried your seed you put in the comments and I get Mystery Gift, as it should be.
I see that you have some mods (like there's a dresser thing in the treasure room), so I'm guessing one of them IS changing item information, and you just don't realize it. For example, if you have a mod that did some small thing to one item, it's possible that it did so by completely copying an older version of the items information to make its small edit.

It is literally impossible for crafting recipes to be incorrect if you're using: The current Repentance patch, the current EID version, and no other mods.

I had this because I had animated items mod installed, after uninstalling animated items its working correctly