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The battery warning light means the alternator is not charging the battery. And the check engine light is probably for the same issue. Have you had the charging system checked ?
if its not fully generating power you will have dim lights and eventually after a while the battery will not charge enough to start the car. not sure of the voltage for a volkswagon but most other cars it generating about 14 on the guage in the car, you can have it tested for free at any decent auto parts place, pep boys, auto zone or advance auto parts to name a few.
problem is that the voltage regulators on the 1.8t which I am sure is the same on the TDI alternator....is that they may work fine when they are cold....but once they warm up is when they start acting up and causing problems. I assume is has to do with some resistor over heating. This is just a common problem noticed by most people over at VWvortex.com.
So you can take your alternator to get tested but if it is tested cold then well it may appear to be working ok. When in reality it is broken. Trust me...it is a cheap enough part and easy enough to fix to not just try it. Some can even change the regulator without taking the alternator out. If you have small enough hands I can see it being done.
I also have a 99 Jetta and I ran into this problem once or twice. How long do you wait in your car after closing the door before trying to turn it on? I've found that the car sometimes will automatically lock itself and engage the alarm system if you are inside of it for over 30 seconds without making an attempt to start it. When this happened to me, I would hit the unlock button on my keyfab twice and then attempt to start the car. Lemme know if this works for you!
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