Assuming the batteries are ok and the remote has previously worked, the only thing that has always fixed this issue for me was resetting the TV to factory condition, then re-pairing the remote. Unfortunately, it does also mean re entering passwords, reinstalling apps etc..
I find owning my Samsung smart tv is similar to using a PC running Windows ME. Works fine then once you connect to the internet and add a few programs it starts to misbehave and has to be reinstalled! I must be on my six or seventh reinstall now. The last time I reinstalled as the smart remote stopped controlling the cable box. I say the control stopped but really it is the tv itself that sends the commands to the tivo etc.. As soon as I did the factory reset the control worked again to change channels on the tivo. I'm afraid the Samsung TV software is proving rather flaky.
Tried everything, resetting, unplugging, updating software, replacing batteries, etc. The only thing that worked was turning the set off using the button on the actual tv, not by using the remote. Now it's back to normal