Nikon D300 focusing system flaw?

After working with my camera for the last 4 days I have to ask; does the Nikon D300's AF system have a focusing flaw? If I shoot my Nikon 50mm f1.4D from f1.4 to f2.0 (one and a half stops) it will consistently focus ahead of the point of aim (POA for shorthand). At 2.2 it's reasonably sharp for its very shallow depth of field (DOF). From f2.5 and on up, it's fantastic! Now that I have the AF system placing the point of focus and POA together at the sensor plane I can finally see some terrific results at wider apetures. Prior to my readjustment, f5 or f5.6 was the minimum I could use on my big Sigma 70-200mm f2.8 lens. Forget about f2.8-f3.5... they don't exist! Now, however, even f3.2 is on the mark, though just a tad soft. I was practicing in the middle of the day. In low light I'm sure f3.2 would be fine.

But this leads me to the great "focus shift" or "aperture shift" question... Is the D300 flawed? I get the same behavior with two high-quality, wide-apeture lenses. One is just a D lens, but it's a well-respected, tack-sharp lens. The other is expensive because it's got big glass elements inside and zooms to 200mm. In my book, both should be useable all the way to their minimum apetures. Through the viewfinder, the images look sharp when focused (don't forget this is with the lens wide open) but when exposed, what you get at the imager varies wildly with changes in the f-stop. If you adjust the camera so that f1.4-2.0 is useable on the 50mm D lens, then the AF is massively pushed too far back at f5.6-f8. I've been doing this for four long days now, in the CA desert heat, confirming results on my laptop, and as sure as a bear craps in the woods, I can reproduce this one hundred percent of the time. I even know exactly how far to turn the AF mirror stop to make the point of focus walk closer or farther.

Now my "kit lens" an 18-55mm f3.5-5.6 lens will do just a little bit of this, but it's wide open values aren't as great as the f2.8 of the Sigma or the massive f1.4 of the Nikon D prime. The only other lens I have to try is a Tokina 12-24mm f4 which has to be "pushed" +20 in the AF Fine Tune setting even AFTER the AF system's been adjusted! It clearly has an issue which will probably require going in for service. Truthfully, I use this lens for precisely two photos with ever car photo shoot. I'm not going to miss it very much while it's away having its tiny electronic brain fiddled with. Besides, it does actually work at +20 and f4, and I gain a ton of depth of field at f8 to f11, so it's not really troubling me. It's the 50mm and the big Sigma I use ninety percent of the time.

So why does the D300 do this? I originally bought a 50mm f1.8 for this body back in 2008, and sold it in 2009 because it had this same trait. I thought it was just a flaw with that Chinese-made plasticky-cheap Nikon lens. Has anyone else noticed this with their D300 or D700 (which uses the same AF system)?