Regardless of what is submitted by DOD to FAA, you would have to report your condition on the FAA medical form under 18-L (Neurological disorders; epilepsy, seizures, stroke, paralysis, etc.) and 18-R/S (Military medical discharge / Medical rejection by military service).

The best thing that you can do is what has been previously stated- get a complete copy of your records, and seek additional opinions/consult OUTSIDE of the FAA aeromedical division.

The folks at Virtual Flight Surgeons might also be of assistance: www.aviationmedicine.com