Rohan Singh
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There is also a topic on the forums which contains a good video of the issue: http://www.minecraftforum.net/topic/1629985-flickering-gui/#entry20291371
A few posts below that shows a very similar issue happening on OS X.
I have been experiencing the same issue. I have disabled threaded optimization for javaw.exe (made sure I selected the correct exe, too) in the nvidia control panel and still see the flickering. Temperatures are well below 60C for CPU and GPU. I have never had these issues with unmodded Minecraft until I tried it on Windows 8. To better describe the flickering, I can see water, far terrain, or the HUD go invisible for a very short period of time. As for switching to fullscreen, that does seem to fix it but it also looks like switching back to windowed will keep the flickerng away.
Intel i5-3550, 8GB RAM, NVIDIA GeForce GTX 550 Ti 1GB (driver 310.70), Windows 8 Pro 64-bit, Java 7 Update 10 64-bit
Still happens for me as well. Minecraft 13w16a (new launcher, of course), Java 7 Update 21, with nvidia driver version 314.22. This was tested with threaded optimization completely disabled (not only for java).