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Hello there! I’m very new here I just recently bought an 05 new beetle.
It runs nice, although I do have to crank it once and pull the key back and then crank it one more time for the engine to start up.
Anyhoo, my question is about the key fob right now.
When I first got the car the fob wasn’t working at all so I figured maybe it was the battery.
I took the battery out, it had a tiny bit of corrosion, I cleaned that off let let it sit and put in a brand new battery. Went outside pressed the unlock button, and the alarm started going off on my car! I pressed the unlock button again, but it didn’t do anything so I manually put in the key to stop the alarm.
I tried pressing every other button, and it still set off the alarm and I couldn’t do anything.
I’m sad! What can I do!
 

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You may have a number of issues going on. If the alarm is going off randomly; the door lock module, maybe failing and so, the car doesn’t know of the door is open or closed correctly. The door lock module; has microswitches that can fail or the solder joints, can crack. The door lock modules; might be able to be repaired but replacement, is probably the way to go. Genuine/oem vw parts are recommended.

Here is a thread; discussing the failures and possible repairs you can try:

https://forums.vwvortex.com/showthread.php?1542461#/topics/1542461?page=106

Here is a door lock module replacement diy:

http://www.newbeetle.org/forums/questions-issues-concerns-problems-new-beetle/109049-window-regualtro-door-lock-diy.html#/topics/109049
 

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As for the key fob working or not; a fresh battery is required and see if the small red light blinks, when buttons are depressed.

Check out this faq; to understand how the key fobs work:

http://www.tunemyeuro.com/vw-key-fob-programming-guide/

Whenever i have had problems with my key fob; i disassemble it and spray some contact cleaner into the switch and press the up/down, to work the cleaner into the switches, to clean the internal contacts. This revives my key fob and the light will blink. I is this contact cleaner (available at most auto parts stores and inder $5 at walmart):

CRC 05103 QD Electronic Cleaner -11 Wt Oz

https://www.google.com/search?q=CRC+05103+QD+Electronic+Cleaner+-11+Wt+Oz&ie=UTF-8&oe=UTF-8&hl=en-us&client=safari
 

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From what you are saying; it sounds like the key fob and the car are communicating but the alarm is going off, when it shouldn’t. I would fix that problem and rhen see; if the alarm issue is resolved.

No start problems; may ir may not, be a immobilizer related problem.

Here is a good page; that goes over the immobilizer system and hiw it works:

https://www.myturbodiesel.com/wiki/immobilizer-faq-and-troubleshooting-for-vw-and-audi-with-key-replacement-tips/

If this beyond your capability to repair or not something, you want to tackle, you may need professional help from a shop that specializes in vw’s or worst case scenario, your local vw dealer.
 

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No start problems; may ir may not, be a immobilizer related problem.
Sounds like the car does run, so I would say that the immobilizer isn't an issue - the car would run for a few seconds and die if it was. I more wonder if there is an issue with the fuel pump/relay which is causing the car not to start on the first push of the key.

Another thing to keep in mind when it comes to the fob is that it could be misprogrammed. Or the buttons could be worn out. You can buy a new half of fob with the buttons and it doesn't require any programming related to the immobilizer. I didn't even need my buttons programmed when I swapped mine.
 
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