Call it in and get your answer fast. Something seems odd with Samsung's design choices in this area and since we can't affect that code it looks to be something you call in, get your answer then make a choice. In my opinion a fine choice is to return the gear when it's found to be defective or just plain wrong.
I have a Samsung PN51F8500AFXZA SmartTV that I've updated the firmware to the latest version (1120). I have a Yamaha RX-A1000 home theater receiver which is updated with the latest firmware. A Mediacom Pace/Tivo XG-1 dvr cable box is connected to the Yamaha on AV2 (HDMI input number 2). HDMI out 1 (with ARC support) on the Yamaha is connected to the Samsung TV on HDMI 3 (with ARC support).
On the Yamaha HTS I have the ARC features turned ON and HDMI Control turned ON. On the TV, I've turned ON Anynet+ (HDMI-CEC), and selected Yes to Auto Turn Off. On the TV, I set the Speaker Setting to Receiver.
With that setup, the TV (and Tivo) remote turn the Yamaha receiver on/off when I press the power button and change the volume on the Yamaha receiver when I press the volume button. When I press the power button on the TV (and Tivo) remote, it turns the Yamaha receiver on and it initially switches to the AV2 input so I get sound, but after 10 to 15 seconds the receiver switches to Audio 1 and I get no sound. So I have to manually switch it back to AV 2. Once I switch it back to AV 2, it works great. Thus with Anynet+ turned ON, I just have to use the home theater remote once to switch to AV2 to get sound.
With this setup is it possible to prevent the Samsung TV from switching the Yamaha to Audio 1? Is there some way to make these devices work together?
If I turn OFF the Anynet+ on the TV, the TV/Tivo remotes no longer turns on/off the Yamaha receiver and turning on the TV no longer switches the receiver to Audio 1. If the TV has Anynet+ turned OFF, the Speaker Setting can only be set to TV Speaker or External Speaker so I can't use my Yahama receiver with my 5.1 Mordaunt Short speakers.
After googling this issue the only solution I have found is to have Anynet+ turned ON, and to buy an expensive Harmony remote that can be programmed to add a delay and another input switch to leave the Yamaha in AV2. See http://forums.logitech.com/t5/Harmony-Remotes/ARC-Anynet-on-Samsung-TV-Switches-Inputs-Automatically/td-p/643198/page/2
My two other TVs are Panasonics, and Viera link on both TVs works properly and leaves the Yamaha in AV2 at startup.
Other than this one very annoying issue I love my Samsung 8500 plasma.