I talked to my doctor and he said: yes, breakthough bleeding is very common on Atkins and that as long as I am taking my pills correctly, they should work just fine, despite the bleeding.
I am taking the generic version of Orthocyclen.

So-- good news for me. And I guess I should say to anyone reading this: be safe! ask your own doctor just to be sure if you have similar symptoms since bodies, histories and pills are all different.