How long did you hold the buttons down? According to the manual, with the ignition on, you have to hold the 1 & 111 (two outside buttons) for 20 seconds. Then you get the middle button flashing. This would clear any previously stored garage door codes in both buttons. Then you can program the "new" code.
I'm not sure what the problem might be if you can't get the middle button to flash.
I found I had to follow a combination of the owners manual and the garage door opener owners manual to program the buttons. It also depends on whether you have an older (probably about 20 years) set code or a newer rolling code garage door opener.