Believe it or not, I think it's an incompatibility between the D3 and some samples the 50/f1.4 AFD. One of my friends has this lens and it does NOT work reliably on my D3. I forget precisely what the failure mode is, but I think that his sample drives to focus the first time and then yields an error code after that. I tried a different example and had it do something different, but it also failed. It could be my camera, but it seems to work fine with the rest of my lenses, which do cover a pretty wide range of capabilities and production dates.
Since I own the 50/f1.8 AFD and a 50/f1.4 AI, I've never looked into this more carefully.
_____ Brian... a bicoastal Nikonian and Team Member
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