I’d guess it’s a software problem, rather than a hardware one, since the software just blindly throws data out of a pin and doesn’t care if you’ve got a HAT connected or not.
I’ll have to investigate and see if I can recreate it. In the meantime, I’m pretty sure a new Raspbian image will get it up and running if you’ve got a spare SD card. A little drastic, but re-imaging generally fixes all woes of this nature.