Security Light keeps blinking, but trucks starts and runs fine

[Koachman1]

I have a 2002 GMC Sierra 1500 with a PassKey system. Not the PassLock system. The truck starts, runs, and drives fine. The problem is when I turn the truck off the security light on the console flashes and I hear a series of 3 quick beeps 3 times for a total of 9 beeps and the security light keeps flashing. 

I thought maybe the old key was worn down and the sensor was not being read properly so I replaced the ignition cylinder but the same thing happens. 

As an aside I am trying to use an OBDII scanner to read a check engine code but when I plug in the OBDII I get a cycle of Low Fuel, Security, and Battery warning lights flashing and the OBDII gives me a message stating it can't communicate. I am guessing the security issue has something to do with the OBDII not working. 

Can you please help me?