I repaired my brakes the other day, but I left the car on while listening to the radio and ran the battery down. I jumped it. Now she is slow to start, the windows are slow to roll up on only battery power and I get a SERVICE THEFT SYSTEM indication on the DIC.
Put a full charge on the battery and then get it load tested. Sometimes when you take a battery all the way down you can damage a cell. A damaged cell will cause the battery to show voltage but not have the amps needed to operate some electrical components.