Anti-theft mode?

I went out to the vehicle first thing in the morning and the car was dead. Key FOB wouldn't unlock the doors, so I unlocked the car with the high security key inside the key FOB. I hooked up the jumper and the alarm went off. I then noticed the negative cable from the battery to the body was very loose, so I tightened it. The battery was at about 4 volts. I took the battery out and had it charged. Reinstalled the battery and when I get in the car with the key FOB and try pushing the brakes then the start button the alarm goes off. The display says "place key in backup position". I tried putting the key FOB in every backup position I could find on the internet as well as on the steering column, but nothing works.