Thanks for the advice everyone. Is it OK to put another coat on even though there are flakes on the first coat? I painted the floor Sunday night, which means that I am nearing the 48 hr mark.
This is an issue of the coating being thicker in some areas than in other areas. Bdamico and Shea talk about coverage issues. They are right on. They talk about stretching the coverage or differing porosity in the concrete. These are two very likely causes. The resolution, as mentioned already, is to apply additional coats of epoxy until you get even film coverage.
As to whether Rust Oleum would recommend applying the epoxy over the flake, I don't know. Call them. The several posts that I have read about this product where the applicator had problems, Rust Oleum was helpful to them.
Personally, I would have no problem coating over the existing flake with more pigmented epoxy and then reflaking. But for me I would do this if I had applied flake rather on the light side.
Regarding epoxy film coverage, the average person, including myself, first looks at the labels and thinks, "Okay, my garage is x square feet, so y kits will give me a professional epoxy floor." Digging deeper, that is not the case. With this product, about 1 gallon of total epoxy product comes in one kit. The percent solids is in the 60% range, if I remember correctly. So about 40% of the thickness of the product is lost to solvent off gassing. Now, add differences in porosity or simply a very porous floor overall, and the concrete "drinks up" the first application of coating.
If you don't have any bare (unpigmented) concrete areas on the floor, you might be able to get away with putting a couple coats of clear over this, which might even out the sheen. Several pros have recommended this in other posts. As Scotty from Legacy said, be sure to roughen the surface/knock down the existing flake with a screen.
