I am having the same issue but it is both my cable box and Xbox One S. I have had my TV factory reset several times, the remote replaced, and a technician came out but couldn't figure it out. Now I am just getting the run around from Samsung. I am not the only one having this issue. You can see it all over the Samsung Community. My theory is that the TV has to communicate with the remote to program it to the correct device but the TV can't communicate with the remote for some reason so the remote is just acting like a standard remote with one-way communication. That is why it can still control the Samsung TV and not the other devices. I have even been told that they don't guarantee that it will work. If that is the case, they shouldn't be advertising this as a "universal" remote.
Update: Issue resolved! Samsung sent out a technician for the second time and I explained my theory that the TV is having a problem communicating with the universal remote to tell it what codes it should be using for the eternal devices. He agreed and decided to replace the IR sensor on the TV. Once he replaced the part and put the TV back together the universal remote started to work like it originally did with both my Xbox and cable box. I hope this helps anyone who is having the same issue and no other troubleshooting worked.