Strange key problem
 

I recently changed my alternator. When I was diagnosing it I got into some kind of menu in the dash by holding one of the buttons for five seconds or so. It has tests 1-20 something. Apparently I changed something because now one of my keys will no longer start the car unless I use the other key, go to test no. 3 and change it from lock then I can put the other key in and it will start. The only problem is I have to repeat this every time I want to use that key. I thought I fixed it the first time but no. Does anybody know what I did and how to fix it?