Okay, a couple of months back i got into a car accident and took my car to the body shop. The remote and alarm was working perfectly when i dropped it off. I get the car back and the remote is dead and guess had been that way for a while. I put a new battary in the remote and it turned on, but doesnt arm or disarm the car. I push it and it just beeps like 5 times and does nothing.

When i start my car my doors auto lock, which is a feature of my alarm so it confussed me. Is my alarm messed up or was my remote dead for so long it just lost sync with the system?

 

why don't you try reprogramming the remote? It depends on what brand alarm it is but for dei's you turn the key on, press the valet switch (within 10 seconds) once, let go, press and hold until siren chirps, press button 1 on your remote, listen for confirmation chirps, turn key off..done.

If its not a dei (python viper hornet newer clifford.....) then you'll have to consult your manual.