I bought a brand new manual transmission '10 Jetta TDI sedan back in December. I currently have 5K miles on it and have followed all of the suggested break in techniques. A few hundred miles ago I started getting a slipping while in third gear. It doesn't happen all of the time, but it is very pronounced when it does. It occurs during both moderate and heavy acceleration. Every other gear is fine. My first thought was the clutch slipping, but its brand new and I've been driving stick for a long time so I doubt I destroyed it that quickly. (This is my first diesel, so I'm new to the mechanical side of diesel cars). I'm assuming they don't have a cap and rotor so that can't be it. No spark plugs, so thats out.
If you slightly change the position of the acceleator pedal at the point of the bucking it should help reduce it. There are also complaints of bucking when cresting a hill. It's believed to be due to engine and EGR tuning.
Also, when I've had a slipping clutch under heavy acceleration it normally doesn't cause much bucking or shaking (most cases that I've felt but yours could be different). It just feels like rpm is fluttering up and down while accelerating (if it's barely slipping) or if the rpm is going up without correlation to speed.
It is VERY unlikely that anything is "slipping." Instead it is probably what others have pointed to: the normal EGR burps which in my experience get less noticeable as the engine breaks in.
But there is a very simple way to test this. Next time it happens, paste the accelerator pedal to the floor. If the revs go up faster than your road speed increases, your clutch is defective. If they don't and the car accelerates smoothly, it is the well-known part-throttle surging described above.
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