Jay Rupp6.7

Batteries died in my truck (2007 ram 2500 6.7 cummins). I recharged them and now one of my 2 keys doesn't work with the truck. it starts it but the anti theft kicks in and the truck goes into limp mode. the other key works almost normally. truck runs and drives, but coughs and smokes a bit now, and milage is down. local delership says they need to reflash it but dont know how or why it happened.
oh and the security light flashes all the time now. tried useing the keys to unlock the doors and set and shut off the alarm. both work for that. unhooked the batteries again (for 4 hours) and rehooked them. no change. no fault codes. Any thoughts on this one?