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This is an issue I've had off and on for, embarrassingly, at least a year:

On misty or wet mornings, everything starts out fine but, a few minutes into the drive (like clockwork. I even know the lights it will happen at), the Check Engine light will flash for 3 seconds and the car starts to struggle as if it was about to stall if I am going slowly or stopped. Driving again, it goes away. Approach another stoplight, hello car shudder. This goes on until about 10 minutes in once the engine temp hits the perfect 90 in the middle. Boom, problem 'solved'.

I would love to know what I should be looking at to fix here. I had previously been told to start the engine while cold late at night in the dark, to look for visible arcing that disappears once the car heats up. Alas, could not find anything. Granted, VWs hide all the important bits, which further complicates things.

Local VW dealers are scammy, so I'm searching for an out of town one to replace them. That said, I'd love to at least have a clue going in so that I'll be less likely to get ripped off again.

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Is this the 2.0L or the VR6 engine? –  Sumo Aug 9 '11 at 3:50
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4 Answers

You didn't mention which engine is in your Jetta, but the Mk IV VWs, especially the VR6 engine, are known to have brittle ignition coil housings that crack and admit water, which leads to misfires.

After the engine has run for a while, it burns off this moisture and it starts running fine again. Some VWs were subject to a recall to fix this issue.

Based on my experience with these cars, the coil would be the first place I'd look. Your description is textbook for a cracked ignition coil housing.

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Though I may not be correct, have you tried opening your hood and using a spray bottle of water on your spark plug wires? Lightly mist around where the wires connect on both ends of the wires, and maybe a few squirts around on the wires themselves. If the vehicle stutters, it may just be that the wires need to be replaced...

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You've almost certainly got a dodgy sensor somewhere. As Bob Cross says, the best way of locating this is to get the OBD-2 code from the ECU, which should tell you which one it is.

I am surprised that it only starts a few minutes in, most such problems I have come across start almost straight away, then go away once the engine warms up. What is happennig is that water is getting into the sensor, or the wires doing to it, and causing it to report an incorrect warning - Once the engine warms up, the water evaporates, so no more problem. If you can identify the sensor in question (I would guess Airflow, fuel or crank position), you may well find that there is a rubber seal or cover that has perished to allow condensation in.

Disconnecting each suspect sensor and cleaning the contacts with a bit of fine sandpaper may well help too, as chances are the contacts will have corroded under the condesation.

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First step, I would take the car to a less annoying shop to ask them to read the OBD code - I would assume that there is one to read if the CEL has been on or flashing. Almost any shop will read the code for you at for a nominal / free charge.

If you would like to know the information on your own, the code readers are common items on Amazon.

I would get that piece of information first before you try anything else.

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