[acidrain]

I'm thinking the surface of your parts was overheated during machining. I've seen this before on other parts... not sure how they got that way, but here is what I would do:
Try alternating etch and de-smut until the parts look more even. If the parts are not glossy enough, you may have to buff them. If these parts have machined tolerances, there may be a problem loosing a couple of thousands of an inch during this process.