This isn't an issue with renaming the inputs, there's a firmware issue on the TV, or at least there seems to be.
We have tried ATi and NVidia cards connected to it, both show the exact same issue, so it's not a video driver issue.
Above illustrates the issue, we've tried 2 brand new clean windows installs, the issue appears right away after driver detection.
I did call Samsung yesterday, after 45 minutes of speaking to someone and having them tell me "the TV is too new, there's no new firmware" etc, when that's clearly not true, since owning this new TV, there's been 3 firmware updates. She eventually passed me on to level 2, I went through the issue with him for another 30 minutes, still no resolution to the issue, however he escalated the issue to the engineers.
We have another slightly older Samsung, a unXX750, we never had this issue, Windows always correctly saw the refresh rates, and there was never a display issue.
I was considering plugging back in the older set to the computer, capturing the EDID from it, and forcing it to the newer set, I was however not sure if this would effect 3D/Arc, so I've not ventured down this route yet.
I contacted Microsoft, they said it's an issue, and contact Samsung. The TV should be defining that only a set of valid refresh rates are in fact valid, this set is saying every possible refresh rate is valid, however if you attempt to output @ 25Hz or 50Hz the Unsupported Mode pops.
This wouldn't be an issue, my media players are smart enough to output what the device supports, I have several PAL recorded sets of media, normally with 50/25 being listed as invalid, the player is smart enough to scale the content as needed and output without any degradation. With the TV stating that 25/50 are valid, I have no choice but to lock the display @60Hz, and not allowing the content to play properly, this is causing a ton of judder/skipping/lag, making all of the content unwatchable.
Removing the AMP from the chain makes no difference either, same issue, we have investigated every possible solution and cause, we keep coming back to a TV issue.