I accidentally pressed the panic button on the FOB, and it set the alarm went off. The FOB would no longer work so I manually unlocked the driver door (by this time the alarm had shut off on its own). I started the car and continued on my way. Now, any time I use the FOB, it sets off the alarm. I have to unlock and lock my doors manually, but my car still starts as per usual. Any idea what the issue is?

 

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First thing change the battery in the key fob.

You need to get your motor scanned (preferably with VAG-COM\VCDS) for any error codes logged in the ecu and post them, that will save a lot of guessing.

Please tell us your car spec in your signature