The switch should be for manual disarm of the alarm. You have to push it a *certain number of times and your alarm will shut off. Like if you were to not have your remote on you and you needed to drive your truck and your truck was armed you could turn off your alarm by using the switch. At least that's what mine is for.
*certain number of times being whatever it's programmed for by the installer. of course their about as easy to guess as a combination lock so don't worry about thieves shutting it off easily. Doesn't sound like a factory alarm but I don't know what Ford thought of for 06's.
From your description it is dealer installed security. You may take a look at your paperwork they gave you when you bought it. It will be listed, not on the factory window sheet, but in the extras you paid for. You can also call the dealer, but don't expect them to be much help. They buy these systems for very little, have some quarter trained kid install them, then charge you big bucks for them.
If you can find the name, you can get the programing information.
If you are VERY lucky, they put in a Powercode.
I suspect it is a much cheaper unit, mounted under the column, behind the kick panel. Hopefully it will have an adjustment. You could probably take it to the dealer and they might be able to adjust it. You may find they had it done at a local stereo/alarm shop.
PATS = Passive Anti Thieft System. i.e. the transponder key aka the key with the big head.
My '06 does not have that switch under the dash.
I did the Ford Silver Remote start, my programming push button is down by the hood release handle, in the LH kick panel. That is to set the way the Silver RMST and the non factory part of the fob for the RKE work ( i.e. I have mine programmed to have a single push on the unlock, unlocks all 4 doors, rather then the factory fob of needing to push 2 times ).
This is a dumb question, but if you use the keypad, would that not disable the alarm ? I would guess the key in the door lock alone would not.
I know in TX the dealers here are installing the KARR make of alarm system. They have a website with a number you can call to get your local support if your dealer isn't helping. Most dealers have techs that are specifically instaling these alarms due to warranty and insurance reasons, check it out. Do you have the keyless entry with the combination key pad on the driver's door? I was thinking about getting the KARR alarm installed but only if the keypad on the door will disable it, let me know.
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