So after spending hours on this I finally figured out why my one remote isn't controlling my CEC-enabled STB, which according to page is because I have Universal Remote setup:
"If an external device has been set up for both Anynet+ and a universal remote control, the device can only be controlled with the universal remote control."
Now, here is the problem. There is no way to disable universal remote (which I believe, is trying to control my STB via IR rather than HDMI-CEC). Even during the initial setup, universal remote is forced and there is no easy way to skip it. I manged to skip the setup after a lot of fiddling and got the remote working properly however, I am now stuck with a huge green nag telling me to setup my device everytime I select it because Universal Remote is not setup properly.
Is there a workaround for this?
And if I could have a feature request for the next firmware update, can Samsung please add an option to enable Anynet+(HDMI CEC) within the universal remote setup? Or just add a skip button and let us save and complete the setup. Come on, it is supposed to be a smart tv and a smart remote.
I have the same problem. When I go to a different input (nintendo gamecube) it prompts for the universal remote setup, but it's not a device that has an IR sensor on it so it can't be controlled by a remote. As far as I can tell after days of searching is that you just have to press the back button every time you switch inputs to cancel the prompt.
If anyone has found another way please post the answer.