DIY transformer (toroid) waveform
(I think answering it myself is better than deleting the question or leaving it unanswered, so here it goes. If anyone has a better explanation I'll gladly accept the answer.)


  TLDR: I had just glued that toroid in particular and the uncured glue
  changed the characteristics of the transformer.


About 18hrs later, this is how the waveforms look like:



Turns out, as I am testing different toroids, I had just wound and glued one to a 3D print with UHU all purpose glue. As it still had not cured and was still quite liquid, I believe it changed the overall characteristics of the transformer. 

I realized this could be the case when I was moving the board around and when my hand got close to one of the "good" transformers, its waveform had changed. Then I remembered that the glue was still "liquid" on the "bad" transformer. Facepalm.