Oh, mystery solved. I had the darkly-red theme on in the brief period between the last update and federation but the federation update broke it in such a way I didn't even notice I still had it on. In the current version it looks almost exactly like the default theme but with the green link text and highlights gone.

I shall amend my request. Please fix darkly-red, it was a really cool theme

This is what links have looked like to me ever since the latest UI update that I believe coincided with federation.