[Smurkey]

It's been my experience and I've read you should use wax and grease remover BEFORE sanding or blasting. The thinking is that if there is any wax or grease the mechanical paint removal can drive traces of these products into the scratched metal. This is especially true of silicone based waxes (which I doubt would be on your floorpans).

A solvent-based wax and grease remover could do this too if it were not TOTALLY dry before painting, as the evaporation of the solvent could form bubbles.

Of course, don't count out the fact the brushing/rolling could be introducing air and the viscosity of the paint is trapping them as it dries.