2001 Chevy Camaro vehical stock alarm system will not arm

HI
I have an 01 camaro that I recently bought a hypertech tuner for, and after installing the program, the vehicals alarm system will not let me arm the alarm immediately after exiting the vehical.I now have to wait a minute before it will let me engage the alarm. It used to be that if I were to press the lock button on the door before I closed the door it would lock and honk twice after the door closed. Now, if I try it, after the tune, it will beep at me like if I still had the key in the ignition, and not let me power lock if the door is open. The alarm will work if I wait a minute or so, than it will let me power lock and arm it. I don't know what else it could be.