Kate,
I don't have a clue why the 1099-misc form is missing in FreeTaxUSA. More importantly, I don't have a clue why it is required. The 1099-misc is required. It is not transmitted to the IRS.
I just enter the total of my consulting business income on Line 1 of Schedule C, and I make certain it is equal or greater than the sum total of the 1099s I receive from clients. (I have one client who always has a error in their 1099. They are usually over by $100-200, but last year they were over $10,000! That's when I have a corrected 1099 issued.)
Cheers,
EarthSurfer