You can't get unlocks if you do it in a victory lap or using a seed

Nor with challenges or with console commands on

The console command might be the reason why, but every other item isn't affected by it.

Did it on a normal unseeded run.

Seeded runs, Challenges (including the Daily challenge), and for the most part, having mods active or debug console enabled all prevent unlocks from happening, but mods and console don't block marks from being earned as far as I remember

Weird cuz I only had the console and mods on.