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Here's what went down this weekend:
My dad and I bought Buggy ('01) a new starter because the one it came with has always made an awful screeching sound every time I start it (it worked well but we were concerned that I'd go to use it one day and it wouldn't start up). Finally had a chance to put in the starter this weekend and BOY was it a PITA.

Anyway, in the long process of replacing the old starter with the new one, we left the battery unplugged for maybe 9 hours... I'm not saying it took that long but we were working on other things under the hood too, so it was powerless for quite some time. Once the new starter was in and the battery plugged back in, we tried to start it. It took a few tries to get it started, but it did start. Almost every time I've tried to start it since, it HONESTLY takes me like 15 tries.

I'm getting really annoyed. :mad:

We read somewhere later that it could be possible that the battery being unplugged for so long could cause my car to forget the matching with the chip in my switchblade key remote/actual key. The weird thing is that my remote works to unlock the doors etc., but its like it doesn't recognize the actual metal key once in the ignition anymore.

I seem to have the opposite of everyone with key problems as far as my research on the org leads me to believe. Everyone's key works, but not the remote. Mine seems to be backwards. My dad says the starter is working and is turning over the engine, but it's like the anti theft kicks in and keeps it from going any further than that and it just shuts off.

I'm desperate. Trying to figure out whether I need to reprogram the key? Or what could possibly be the problem?!

If it makes any difference, I have an aftermarket stereo installed, but I've never had this problem until after replacing the starter.

HELP ME (please)! And thanks in advance to all you geniuses who make bug life easier. ;)
 

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When the battery; gets low or is not hooked up, the immobilizer can get goofy and cause problems, essentially gets "confused" about which key is matched to the car. I would start troubleshooting the problem; by removing, the pos/neg cables and touching them together for thirty seconds, this will do a hard reset of the computer. See if that helps; other then that being the problem, you need to figure out what is actually wrong. The remote portion of the key and immobilizer, are two different systems; so one can work fine and the other not. A low battery; will cause immobilizer problems, I would have the whole charging system checked and make sure it is working ok. I would also; have the car scanned for trouble codes and see what they say, you most likely will have a bunch... because the battery got run down and every computer in the car, was not able to work correctly with low voltage. Save the codes and clear the codes, see if any come back... after the battery/electrical system are fully charged. Worst case scenario; you might need to have the keys "re-matched" to the speedo cluster/immobilizer; using a program like VCDS or have a dealer do this for you.

When you start the car; does it start and then seconds later die, with the immobilizer icon blinking in the speedo cluster? That, would be the classic case; of the immobilizer kicking in and stopping your car from starting. If you have another key; you can try them and see if the problem goes away or leave the key in the ignition (on) for awhile and that usually will cause the immobilizer, to reset and then start. If this is the case; it will usually throw a code "engine blocked by immobilzer".

If it isn't starting: there is no immobilizer icon blinking in the speedo cluster, then you have another problem. This most likely, not the immobilizer and you need to check other things that would explain the no start or hard start issue. I would check fuel pressure, charging system, and/or speed/crank sensor; many times a scan might show a code, to put you in the right direction of the problem.

This page: discusses immobilizer issues and walks you through, the typical issues related to it, how to start troubleshooting the problem:

VW and Audi key, remote, and immobilizer FAQ and troubleshooting
General introduction


Immobilizer FAQ and troubleshooting for VW and Audi, with key replacement tips | VW TDI forum, Audi, Porsche, and Chevy Cruze diesel forum
 

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What was the source of your starter motor? Did you bench test it before installing if it wasn't new?

First rule of troubleshooting a new part, assume the new part is the problem.
 
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