First of all, I'm so glad you read your medication sheet. You would be suprised if you knew how many people don't. I know you have had a lot of help already, but I hope this helps. Flagyl is a catergory B pregnancy rating. This means that when extremely large doses where giving to pregnant mice, the fetuses were not harmed (yes, that is cruel, but they can't test on pregnant woman).
Flagyl can also cause neurological problems in adults, seizures and numbness (this is probably the contradindication that you read on your med sheet).
It also crosses the placental barriar (which means your baby will receive some of the medication).
Because, most of the nerological development of the fetus happens in the first trimester AND flagyl can cause neurological complications in adults....the FDA automatically say do not take the chance unless you have to, even though all animal test show that it was safe.
PS. If you have trouble getting answers from your doctor about medications. I would speak with your pharmacist. They can probably give you a better explanation about the medication and help you make a decision.