You didn't expect it to keep the CPU cool with that chassis thickness, did you?
Macs (except Mac Pro) aren't machines for graphic-intensive gaming.
The 680MX will run it with good FPS, but the machine WILL get extremely hot, no matter what you do.
It's a choice made by Apple. Form over technical performance (which involves temperatures and speed, too).
If you want a machine to game without worrying about temperatures, you need to build your own computer (or just pay for overpriced Alienware things).
As for your current issue, it maybe some Windows driver not correctly installed (I highly doubt on that, since the cooler was working fine before, as you said).
It might simply be a problem with the cooler or the Windows installation itself.
Reinstall drivers. If the problem persists, format and install Windows again.
If the problem is still there, you have your answer.
I see you've never actually used one.
The case is thinner than the previous generation iMac, yet the temperatures went down due to a combination of better thermal design and more efficient CPU+GPU combo.
With the fan running properly both the CPU and GPU run well inside the thermal envelope they were designed for (i.e., a good margin under tjunction). Just because the case is thin doesn't mean this is not possible.
I can work the 680MX hard (skyrim, bioshock infinite, metro etc etc all on ultra settings) for hours without the temperatures getting close to that, but the fan needs to ramp up.
I have never had a situation where it didn't do this, but it seems like some people do for some reason (didn't install the bootcamp drivers? problems with install? no idea).
The idea that the machine runs hot just because it is thin, or that the performance is compromised because it is thin is just totally unsubstantiated nonsense that is not backed up by the reality.
A PC with a poorly-operating cooling fan will behave in exactly the same way, even with a giant "airy" case because they're fundamentally operating with the same engineering challenge - the area that generates the heat is a small square the size of a postage stamp. The relative sizes of the physical case that these tiny squares sit inside don't matter so much *as long as the ability of the cooling system is adequate*. The one designed and fitted to the iMac is more than capable of handling both the CPU and GPU under maximum load for hours without any danger of overheating.
If your CPU or GPU is getting close to thermal shutdown then the fan has not been increased properly. This is not a flaw in the design, it is a failure of the software to respond to the demand (also the hardware will cut in with protection measures before the thermal shutdown will - the SMC can ramp the fan itself, and the CPU itself can throttle against the wishes of the OS).
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I m planning to play games on windows via boot camp on my late 2012 27" iMac, so i should get a fan control software & tun up the rpm when gaming on windows? anyone else having issues with fan management under windows 8.1 64bit?
Thanks..
I have never needed a specialised fan control app under Windows. I use the Late 2012 i5 iMac with the 680MX with Windows 7.
I have the bootcamp drivers for my system installed, and use GeForce Experience to keep the Nvidia driver up to date (the one included with bootcamp is from nvidia, but it's an older one).
I have never had temperature issues despite heavy gaming under windows. My advice would be to install Nvidia Inspector (or some other app that can monitor the temperatures) and have the monitor running while you tax the machine. If you find that you're getting close to the thermal limit of the GPU/CPU then you need to look at the fan control. Based on my experience, I have not needed to manually control it. I have owned this machine since December 2012 and it has been in heavy use since then without issue.