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You do need to take it back to the dealer and get it reprogrammed. I have had trouble with my 07 system from the start. My system will not recognize my fob unless the batteries are super fresh. They only last 1-2 weeks and then I have to disable the system with the code for it to start. My fobs have been replaced and that did not solve the problem. I posted the issue here and found that most folks go a year or more before changing the batteries. Bottom line is the system does indeed need to sense the fob before it will allow you to start it......
Another nice thing about the security system is that when it arms itself you get 2 chirps...sorta lets you know it works. Same when you unarm..more chirps to let you know its unarmed. This sequence has to be set up, it's in the manual.