I opened my car door with my key instead of the keyless entry and for some reason my factory alarm went off. So I tried it again with the spare key and it happened again. What's going on?? This was the first time I used the key instead of the Keyless entry. Has this happened to anyone else?

I don't have an alarm nor keyless entry in my GXE but.....

Are there different setting for the alarm if you want to use the key vs. keyless entry?

thats because when you open your door with your key the alarm is still on.

When I open my GXE with the S&C package with the key, the alarmn is disabled.

Happened to me,
 

but it is only when I unlock the passenger door w/ the key and open it. If I unlock & open the driver side, there is no problem.
This is actually how I figured out the car had an alarm to begin with; and I hadn't recieved the remote thing yet...

the only thing I can think of is you've either got a bad switch in the key lock (that sends a signal to the factory alarm to disarm it), or the person who installed the keyless entry cut that wire or otherwise fudged it up when it was installed..

or do you have factory installed keyless entry on your car?

Factory installed Keyless entry.
It's weird, both keys that I got with the car will unlock the door, but when I open the door the alarm goes off. It doesn't bother me too much because I always use my keyless entry, but I have some spare keys and if I ever have to use them....it'd be a pain!

I agree 100% with Matt. Take your panels-->>
 

off and see if switch is connected right. Also, in the Service Manual it tells you how to test it.