I had a similar problem the other day. Fob didn't work so I opened the door with the key. Started the car and then because the fob was in the ignition it reprogrammed itself. Went to lock the car 10 minutes later and the fob worked fine. This is the second time that it's happened to me and the first time neither fob worked but I was always able to start the car. I figure the BCM had an electronic hiccup of some sort. The other time it happened was about a year ago.