I have a 2000 f350 dually with the 6 speed manual transmission and am growing concerned about a grinding noise. The clutch is still strong and a few mechanins said it was fine but I keep worrying about it. It only happens when taking offf from a complete stop and happens right when the clutch is released. Is doenst occur at any other tima nad the other gears are fine and the truck shifts smoothly. Is this normal? Any idea what is causing the sound?
It's called "gear rollover" and it is totally normal. I'll try to explain it as best I can.
It is pretty common knowledge that a diesel engine typically makes more horsepower/torque at lower RPMs than a gasoline engine. My diesel pulls as hard at 1500 RPM as my old gasser did at 2500 to 3000. What this means is that each power stroke, in and of itself, must create a lot more power in a diesel than in a gasser, because there are half as many power strokes at half the RPMS, making the same power.
What this means is that the power output of a diesel engine is not very smooth. The rotational force at the crankshaft has 4 pretty impressive surges per revolution. That is one of the major reasons why transmissions that will live for 200K miles behind a big block gasser will croak after 30K on an oil burner (which Dodge and Ford found out the hard way, and caused Chevy to te-think the 4l80E coupling tot he Duramax in 2001). The quick succession of fast, powerful surges at lower RPMS creates a sort of vibration in the transmission, causing the gears to "chatter" against one another, thusly creating the noise you are hearing. You don't hear it at higher RPMS because the time between the surges reduces, and the chatter smooths out. Also, under less load conditions, the surges aren't powerful enough to cause the chatter, so it goes away.
The old-style OBS trucks with the ZF-5 had a dual mass flywheel to try and smooth these surges out, and let the ZF-5 live a bit longer. The newer Super-Duty trucks have a ZF-6 transmission, built, designed, and packaged to live their entire 500,000 mile life coupled to big, medium duty diesel engines liek the one's in our trucks, only on trucks weighing one hell of a lot more than our trucks do. What that means is that your truck will be old, rusted, and busted before you need to worry about your ZF-6 going south on you, as long as you take care of it.
That being said, the gear chatter (rollover) noise gets worse as your transmission fluid ages. If she is pretty loud right now, and you haven't changed the juice in a while, you might consider changing it out soon. I used a full-synthetic ATF and it really quieted it down.
So, in summary, take care of your transmission. Change your fluid every 30 to 50K, and quit worrying!
I hear quite a few people describe this with the 6 speeds. Now I know how to explain it. 
