I'm actually surprised to hear this. I help buyers purchase new construction quite often and one of the great sellings points for many builders is the guarantee that you're getting a great deal. In fact, I've even had some contracts have a clause in them that states you'll purchase the house at the fair market value at the time of completion along with rate locking.
So, as my colleagues have stated, how does your financing contingency read? In a standard Florida Association of Realtors contract, your financing contingency states that not only do you have to obtain financing at or lower than certain terms, but the home itself must appraise. And, as a buyer, you are legally allowed to have a copy of the appraisal...is this something you have in your possession?
Essentially, this all boils down to how your contract is written. If you went in to a builder without an agent, now might be the time to hire an attorney, or consult and agent you trust. If you have a Realtor, they should be aware of your financing contingencies and should be able to protect you at this point. Most of the builder contracts are pretty iron clad and protect the builder, so if you feel you cannot mediate this value issue on your own, again, consult another RE pro. ;)
I am also concerned as to how a financial institution will justify you obtaining a loan amount over appraised value, unless your down payment is so significant it negates that? Let me know if you need any help. I know it's frustrating, but as a buyer you hold a lot of cards right now-don't be afraid to pull out the big guns when it comes to negotiations.