Yeah, that's why after they were powder coated I lightly sanded/filed them back to the bare metal on the hubs to make sure the surface was flat.
Chris
I had my discs off so many times my hub surfaces were also spotlessly clean as well, i also bought new discs and managed to buy some very cheap used discs as well and kept rotating them on the bike in desperation to try and sort things out, as well as scrubbing the disc surfaces, and different types and makes of pads.
I have 98/99 forks on my 2000 bike, without the adjusters, which i personally thought were useless anyway, and i believe my wheel bearings were replaced too.
Oh, and the steering head bearings were changed too (not a fun job). You've not mentioned head bearings, i presume you've checked for any play?
When buying new discs it's very important to remove the protective film that's on the discs with brake cleaner until they are spotless, bit late now but thought i'd mention it anyway! You can try and burn it off by hard braking but can presumably contaminate the pads with it.
My calipers were serviced by me 2 or 3 times a year, that's why i got a bit good at doing it because it was so often.
So, as you can see, a very similar, very frustrating scenerio.
I still think the brake lines could be the culprit, in one way or another, but that's me probably being a little biased. Whilst i did all this myself, i also had 3 or 4 mechanics evaluate it too, and they couldn't figure out the problem either, it was 2 of my mates chatting who suggested changing the braided brake lines, but in fairness there was really nothing else left to suggest as it had already been done!