Runes never drop after update to Afterbirth+: bug or bad luck?

I have all runes from classic The Binding of Isaac: Rebirth challenges unlocked, and while I was playing Rebirth, they dropped with regular frequency. However, after installing Afterbirth and Afterbirth+ updates, and playing quite a few runs, I haven't seen a single rune drop. The challenges still marked as completed on "Challenges" page.

Could this be a bug introduced by the update? Is there any way to test the fact that a pickup is properly unlocked?

The easiest way to test is to find a seed that you know will contain a rune early on, and play it. If the rune doesn't spawn, something is stopping it from spawning.

Assuming you have Jera unlocked and are playing on PC, try E8XS 8371. The Jera rune is in the curse room on Basement 1.