Nikon D90 autofocus problems?

I had autofocus woes and sent the D90 back to Nikon. They charged me 250 bucks to fix it and it was perfect for about 500 clicks and now its crap again. Why does the camera use the focus motor in the body and not the one in the lens? I never hear of D40/60 owners with focus problems cause they have to use the motor in the lens. Anyway, I've 86ed the D90 and stepped up to a D300S after hearing of D7000 and D600 horror…

I don't know exactly why your D90 is messing up the auto focus. The fact of the motor in the body should not be causing it. If the lens on the camera is an AF-S one, then the motor in the lens is the one being used. Those lenses do not have a mechanical link to the camera's autofocus motor drive. The camera's autofocus motor only comes into use when the lens on it is an AF-D.
Have you tried taking photos with live view? If the camera will autofocus accurately in live view (using the contrast detect autofocus sensors) but not in normal view, then the phase detect autofocus sensors are malfunctioning.

If it is using the focus motor in the body, then you are using AF lenses. The D40/D60 cameras, even the D3xxx and D5xxx cameras can't even focus AF lenses, they can only autofocus AF-S lenses.

And you may simply have a lens that is not calibrated correctly, especially if you have an older AF lens - as it seems you favor older equipment. Maybe you are buying abused junk.

And I don't know what D7000 and D600 horror you are hearing. I have a D90 that has given me 4 years of exceptional service, with 10 lenses - 5 AF lenses and 5 AF-S lenses. No problems. I recently gave my D90 to my son when I bought a D7100, which is also exceptional.