There are two VAT settings in the admin Customer Configuration:
Create New Account Options -> Show VAT Number on Frontend
Name and Address Options -> Show Tax/VAT Number
If I turn them both on, then the customer sees two VAT inputs while registering during checkout! Why are there two?
the field from the Name and Address Options was used before Magento 1.7 which introduced the new address based field. I think Magento left this for backwards compatibility.
I think you only should use the address based field, this field is also used when you use the Magento core VAT validation functions.