Backup of manual:
Programming Your Access Code
There is a soft “beep” sound and a brief light with each keypad entry. Enter the factory-default, from left to right: one, two, three, The door will open.
Leave the door open. Find the Learn Button (see above).
Press and hold the Learn Button for two seconds. You should see the green light and hear the two-tone beep – the unit is now in “learn” mode.
Enter your new code. The light will remain green. Press and hold the Lean button again for two seconds. The light will turn red, and you will hear a beep. Release the Learn Button. While the light is red, enter your new code a second time to confirm it. Press and hold the Learn Button a third time for two seconds. Release the Learn button. The light will blink green five times. And you will hear five beeps, confirming that the new code has been accepted. If the red light blinks three times with three soft beeps at this point, and error has occurred. Just start over by depressing the Learn Button for two seconds.
help from someone else:
Yep. Been there done that. Start by pulling the batteries out for a full 30 sec. Replace the batteries and start over. Press the "learn button" per the manual and follow the rest of the instructions. When you enter the code you need to do it quickly and press the "learn button" within 5 sec max. I called them the first time I tried to program the safe and the gentleman said that the unit will become "confused" with multiple attempts to program. Pulling the power will reset the unit and allow you to program the code. I used one hand to hit the learn button and other to enter the code. Good luck. If you still have issues, give them a call. They are part of Cannon Safes now.
Notes and help from http://www.thehighroad.org/showthread.php?t=206245&highlight=vault