I always put one of our two OOP maximum amounts in our FSA

This way, I know that at least 50% of our potential total hospital/doctor visit expenditures are covered for the year and we save a little on the taxes. The rest, we just cash flow.
Between prescriptions and co-payments, I know it will all get used by the end of the year with no problem. This year and last, we blew through it in the first two weeks of January (darn dialysis!)
Now that by the grace of God, I have received a kidney transplant, I think it will take us a lot longer to go through the FSA money during the course of the next year, especially since I will be covered by Medicare primary starting in October until April of 2016.
To answer your specific question, I do not treat FSA reimbursements as part of the debt snowball. If I have extra cash and pay the medical bill without needing to replace that money in another budget category, then I might put it in the snowball as an extra payment.