In summary I have a new Samsung ue43u7100 and a virgin V6 box. When I first got the tv, I was able to control both the v6 and xbox with the Samsung remote after setup (it failed the first few times, but then just magically worked). After a week of working perfectly, it stopped working as an universal remote. I can still get the tv image on the hdmi, but the remote no longer works.
I have tried-
Resetting tv and v6 to factory settings
Samsung helpline. They took control of the tv remotely and confirmed the tv and HDMI ports are working correctly.
4 different hdmi cables in both ports.
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