I had the same problem with my remote. The remote suddenly stopped working. After replacing the battery, the remote still did not work.
I tried resetting the reciever with the SRT button. The reciever still would not recognize this remote (it does recognize my other remote).
I also checked out the two remotes on a spectrum analyzer. Both transmitters were on frequency at 390MHz and transmit at the same power level. The main difference was with the data being sent. The good remote appeared to be sending random data (security codes), while the bad remote repeats the same alternating patterns of 1's and 0's.
After all of this, I called the craftsmen garage door opener hotline at 1-800-528-5236. After talking to a supervisor, they agreed to make an "exception" and send me a new remote for free if I agreed to return the bad one.