Problem between Afterbirth+ and Repentance

[Neisan]

Hello, I'm experiencing a bug only with The Binding of Isaac: Repentance. I started with the base game, The Binding of Isaac: Rebirth, and I didn’t encounter any bugs or issues. Yesterday, I bought all three DLCs for Isaac, but in the Repentance version, I'm forced to start from scratch with no option to recover my Rebirth save file. There’s no progression: whenever I beat Mom for the first time, I get the cutscene, but the game tells me I haven’t defeated her. All the items I picked up during the run are considered “not yet obtained,” and this happens even when I complete a challenge.
Also, the mods I installed were already available from the start (for those who don't know, you're normally supposed to beat Mom once to unlock them).
For now, I'm playing the Afterbirth+ version without any issues.
Can you help me fix this bug, please?

[Nazemec]

Originally posted by Neisan:

Also, the mods I installed were already available from the start (for those who don't know, you're normally supposed to beat Mom once to unlock them).

Incorrect. You can use mods immediately.
However, having any mod or the debug console enabled on a new save prevents all unlocks. (Specifically, until the Womb floor is unlocked, first Mom kill.)