Steve,
Sounds like you have the infamous back focus problem. I think when you get it back from Nikon, all will be well; at least it was for me. One possibility that has been bantered around as a cause is casually waving heavy long lens around by the camera body rather than using two hands to support the combination while moving around. I have no idea if this is the true, but I have not had the problem since I got my camera back.
I hope you enjoy using your D1X as much as I have. It amazes me that three year old digital technology can still stand up so well. It has also saved me a lot of money. Of course when the D2X arrives, I will be first in line emptying my pockets into Nikon's bank.
Regards,
Henry
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