Hi everyone, I've had the exact same problem with a D90 and Metz 50 AF-1. Here is the thread I had opened:
http://www.thephotoforum.com/forum/lighting-hardware/275089-built-flash-firing-off-even-if-i-set-off-commander-panel.html
I'm afraid that, even if you set the Commander to "--", it will still emit a little flash of flight and yes, it will be when the shutter is open. See this picture:
However, it will be a very weak pulse and, in normal conditions, it will not affect your pictures. When I say normal conditions, I mean two things:
1) Reasonable aperture and ISO. As soon as my Metz was delivered, I started playing with lighting, making portraits of oranges and apples with hard or soft light, different angles, etc... At ISO 200 and F4, I did not see the built-in flash at all. However, at 3200 and F/2.8 with a close subject, it might get in the way.
2) Reflecting surfaces. If you have a reflecting surface right in front of you, perpendicular to the direction you're shooting and very close to the camera, you'll see the built-in flash. See this picture:
However, you can solve this problem by putting something in front of the built-in flash. The "something" can be a proper Nikon accessory (
SG-31R IR Panel for Built-In Flash from Nikon) or a piece of paper stuck between the body and flash, which is how I shot this:
Bye bye!