Is there any reasonable explanation for this phenomenon?
I have same experience with my 46F6400 and STB (it is labeled as T-Home Media Receiver 300, but it is Motorola VIP1616e). Samsung Smart remote was fully functional even without the original IR extender cable, I was able to switch on/off the STB, change channels, show EPG etc.
BUT - last week I have purchased a new yamaha AV receiver and with the goal to make a new (fresh) setup I disconnected every piece from my audio-video equipment (power cables, hdmi cables from my TV, STB, old AVR, Bluray). Long story short - at the end I have lost the ability to control STB with the Samsung smart remote, even with the IR extender cable (TV and STB are connected with the same cable in the same way). I tried almost every possible configuration, but with no luck. I will try to reset the TV, maybe it helps.
So my lesson from this story is - never change a working configuration. I really dont know, how it was possible that I was able to control STB with the Samsung remote even without the IR extender, but it worked.
(Sorry for possible language mistakes, I am not an English native)