The 9960 is a very old remote, and it uses 3 digit EFCs. You can easily see that in the Lookup Tool
when you select UTC-9960 as the remote model. So for a IR protocol like NEC1, which only uses 8 bits of data, you can enter EFCs. A protocol like Sony Combo needs 16 bits of data, and you need a remote that accepts 5 digit EFCs.
The 9960 is a JP1 remote, and requires a different cable (or the recently available adapter) than the Atlas or Comcast remotes.