The information I read indicated that the FSA deposits are included as part of your COBRA insurance premium. In that case, since you are paying the premiums from after-tax dollars, the entire insurance premium is an eligible expense to deduct as a medical expense (subject to the 10% rule of course.)
The net effect is that you are taking a tax deduction for after tax dollars being put into the account where they mingle with the other pre-tax dollars, in the end, all the money in the FSA ends up be pre- or un-taxed. Then any costs that are reimbursed from the FSA are not eligible medical deductions because they are already paid with tax-free dollars.
If you end up not actually being able to deduct your COBRA insurance premiums paid with after tax dollars because of the 10% rule or because you don't itemize deductions this year, there's no other way to get the money into the FSA tax-free.
