The problem is that the ectronic aperture control is systematically off by half a stop. i.e. 1.4->1.4, 1.7->1.4, 2->1.7, etc. I suppose the widget that controls this was installed with a small offset inside the lens. The manual aperture ring is accurate however, and my D700 is configured to use that instead now.
What's sad/funny is that this is only an issue because it's a ZF.2 lens; I would have been perfectly happy to buy this as a ZF.1 and would have nothing bad to say about this copy right now. This is the first time something like this has happened to me (getting a bad product) and I'm annoyed that it happened to be a Zeiss lens -- the inspection certificate for the lens was signed despite this, so it's kind of meaningless.
The good news is that it is the first f/1.4 lens I actually want to shoot at f/1.4.