I think the reason could be just that my Iodine dosage was so small (under 1 mg). I am taking the accompanying nutrients also so I don't see it being detox at this dosage.
Now that I bumped up my dose to 12 mg I've been feeling much better. It's only been a few days so we'll see.
Perhaps I woke my thyroid with the small Iodine dosage and it just wasn't getting enough.