I'm not sure about the direct effect, but I'm positive you will notice an effect if you get pregnant. LOL
I was told by my pharmacist that there is a possibility that taking my birth control will lower the potency of the thyroxine I'm on. Basically that the b/c somehow makes it so that the thyroid meds are less effective than they would normally be? That's how I understood it at least.
Definately talk to your doctor to see if it could help. Although then you would be left w/o birth control..