A medical FSA is not reported on your W-2. In fact, it is not reported anywhere on your tax return. (This means, for example, there is no penalty for misusing the money. This is because the IRS places the burden of compliance on the plan trustee and not you.)
If you list your medical expense deductions, Turbotax will ask for all your medical expenses, then will ask for all your reimbursements (including regular insurance, FSA and so on). This is not because the FSA is reported on your tax return, but because Turbotax is designed so that you will simply enter everything and let the program figure out what do with it. Medical expenses paid from an FSA may not be used as a tax deduction since they were already paid with tax-free money, but the program is designed to do that for you.
