Same problem - Dealer fixed it (so it seems)
We bought a new 2006 TDI Jetta in May and had the same stalling symptoms from 600 miles on (to 900). We have an Automatic, NOT manual though. It would be hard to start, and stalled a few times when coming to a stop. The dealership was less than helpful and said they had never heard of this. We printed off the posts on this forum and then they agreed to look at it. There were two seperate service times as described below. They had the car for 8 days total. - BTW - The fuse panel layouts in our car, Manufactured 12/06, do NOT match the manual, and the Dealer had no updates.... many of the fuses were loose, but this was not the problem.
Another friend of ours had the same car, same problem, similar fix (fuel pump) to ours...
The SHORT answer: Fuel system problems.
The LONG answer:
** First Service: (After two weeks of trouble) The head mechanic looked at the car, opened the Fuel filter top and told us the we had put GAS in the car, and it would not be covered under warranty. We produced the receipt from the *ONLY* time we filled up the car since we bought it, which clearly had DIESEL written on it. 3 people at the dealership then admitted that the car could have been topped of with GAS -by them- upon delivery. They said it happens all the time... (hmmm...). Either way, they purged the fuel system, and returned that car (under warranty / covered by dealer).
** Second Service: The next day, the car died and would not resart at all. We had it towed to the dealership. The dealership did not look at it until the next day, and it started right up. We explained our disatissfaction with the service, and they agreed to look at it for a few days. They found a shudder under rapid Accel/Deccel and decided to replace the "tandem" (sp) fuel pump (near the engine). Better, but it still had problems. Then one of the youngest mechanics decided to check fuel temp at various points. Turns out the fuel was boiling before it reached the injector system due to some kind of partial block in the return line causing back pressure. The fuel would not flow fast enough so it got too hot. They purged the fuel system again, and cleared the block, no idea what it actually was, and since then no problems.
** Result: Fuel Pump replaced, partial -unknown- block in the return line, and had Gas in it for a short time. Any or all of the above. One thing the head mechanic did finally say: These cars are VERY sensative to fuel line/system issues, and will stall far easier than their gas counter parts if there is a minor problem with the fuel system.
Diesel engines only need fuel and air to run, so unless your car sucks a tennis ball or a squirrel into the air intake, it's a good bet it's the fuel delivery system if it's stalling... ...and it may not be easy to track down...
Good luck to all of you with this issue...