It may be that the silicon did not permeate your paint but that you just moved it around by sanding, etc. without first getting the surface clean. You might try a product call "Poly-cracker.
I think you'll find that if you have used Armorall or any similar product in proximity to the area you are trying to paint, you will experience fish eye. Wet coats are especially troublesome. You might solve the problem by putting down multiple, light, dry coats.
It took me 3 weeks of putting down light coats every day to solve fish eye on the black painted areas of the dash in my wife's '67 Impala SS--the result of the PO using Armorall on the interior for 15+ years. I thought I'd never get it right!
