id would say that the flakes are possibly just evaporated residue. If the area where the flakes are found are not pitted in any way, then its probally not rust. when the ususal tap water is put into the engine, and then left for a while, the water can evaportae leaving behind the disolved minerals, hence the brown and white flakes.

The brown is probally iron and the white, calcium.

Clean it out, look for pitting, and if all clear, go from there.