Just received my repaired Air this morning with replaced screen. Lines are still apparent, though not as strikingly visible as last time, but eye strain kicked in fairly quick even with the dimmer lines. I took it to the Apple Store just for the hell of it, and the Genius there immediately saw the lines. We checked the display model on the floor - also lines and at about the same intensity of my new screen.
He told me it was a screen matrix issue. I don't know what that really means, but that's what he said. He took the computer in the back and said there were no lines on the external monitor. He was quite shocked that applecare had attempted to repair my computer rather than just send me a new one. He said I could ask for a replacement, but he was not optimistic that it would come back without lines. He implied that this was part and parcel of the particular backlight technology interacting with the lcd crystals used on the Airs, which is different from the technology on the macbooks and the pros. His theory was that the eye strain was a result of my subconscious focus on the lines, which may vary in intensity from screen to screen but that are probably on all airs, and since I have excellent vision and now an awareness of them, I will probably always see them.
Long story short, I'll be returning my computer and asking for a refund. I really wanted the portability of an air, but this is intolerable, especially when the price tag is $2,500. So macbook here I come.