Hi there.
I think your observation is something I have as well.
I was on atkins too. And it seems that when I was on atkins my pimples didn't break out too many. But they were still there though.
I was reading on atkins and found out that too much refined carbs can actually accelerate the growth of these bacteria and other fungi.
So maybe what we observe is scientifically logical.
Are you still on Atkins? if you are you can go to this site to sign up for the free newsletter. They give away ecookbooks. just go to http://www.cookie4thought.com. do not buy anything there. just scroll down, and sign up for the free ecookbooks.
The first ecookbook was healing foods worth about $100 or so. I got it free in my email. So I hope it helps.