I know this thread is a bit old by now, but I haven't been around in a while.
Anyway, I, too, have noticed a problem with apparent backfocusing of the body. No matter what lens, aperture or lighting condition, most images are just slightly out of focus. I've tried stationary objects, using a tripod, auto-timer and shutter-up delay - and still out of focus. I've tried apertures past f/15 and still out of focus. Shutter speeds upwards of 1/1600 and still out of focus.
I've tried everything I could possibly imagine and have tried making changes, suggested by oter users. I firmly believe that there may be a few samples of this body that just don't focus correctly.
I sent my d90 to Nikon about a month ago and they seem to have corrected my back-focusing issues ...