I have created a shipper and then tested the info that I submitted and I am getting a standard rate of $12.99 for shipping. I don't even see this fee in the shipping module. Any idea why this is happening?
To configure shipping rates, in VM admin go to Store/Shipping module list and under the name "Standard Shipping Module" is the link to configure shipping rates. While you may not have $12.99 there, do you have a figure there that when tax is applied will be $12.99?