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I have a 1999.5 Jetta that I recently purchased, and I am trying to get accustomed to some of the issues. The car has 126,000 miles and a fresh injection pump/timing belt change. The car scans and shows no codes, and runs beautifully.
I have been reading, but have not stumbled upon the issue that I am hoping to resolve. Please accept my apology, if I am asking something that has been addressed already, and just have not been able to find so far.
The car starts easily when cool or cold. I live in Southern AZ and normally do not see temps below 40 degrees most of the time. Even at 40 it starts immediately, or at least by only turning over briefly. However, if the car is shut down for a few minutes once fully warmed up, it will require cranking for an extended period of time(5-10 Seconds or more). This is only when warm/hot, and not if the car has sat for an hour or so, or started fully cold. Where or what should I possibly start looking to find, or is the normal for these engines? Surely does NOT seem like something that would be normal to me, but then again, I have never owned one of the TDI diesel engines, only archaic American iron. The American iron always has started more easily when warm than cold.
 

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That should be the case. Often hard starting when cold is due to a faulty coolant temp sensor. Unplugging its plug forces the glow plugs to max (and sets an error code). However, a warm engine doesn't need glow plugs. Try unplugging it just in case the sensor is bad and there's something weird going on.

Is the battery charge OK?

The obvious thing is that the timing belt timing is off so that it's out of spec when warm but OK when cold. You must use a vag com tool (now called VCDS) to look at what timing the engine sees. It's possible it's the cause of the problem. Also check the injection quantity. My guess is that it's related to the injection pump or timing since you just had those done.

Another possibility is a fuel leak. This normally happens on cold engines, not warm engines. Diesel shouldn't vapor lock either.
 

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Discussion Starter #4
Battery is new, replaced in July of this year. As for the injection pump timing, I know that the mechanic that did the timing belt and injection pump is quite familiar with the cars, and said that the timing was set with the computer, and was spot on.
I can ask him IF he checked it both cold and hot, but the car seems to run way too well, and start WAY too easily for me to think that there is a timing issue. While I have not owned the car for long enough to check the mileage, the previous owner said that he was seeing an average of 46 MPG on his daily commute, which was a mix of about 10 miles of straight highway, and 4 miles of neighborhood and in city driving each way.
 
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