I recommend Aervoe Industries Insulating Epoxy Coating for coating Flybacks and HV coils, perhaps prior to coating them with Wax or Silicone.
It has a rating of 2100 volts per Mil of thickness, probably well in excess of the voltage difference between individual turns of a Flyback. Also it's watery thin so it can flow deep into the windings and seal them.
http://www.aervoe.com/paints_coating...y-Coating.html