I had to switch my grub configuration to boot 2.6.32-358, the differences in the 2.6.32-431 headers are what cause the duplicate errors. But, if as you said, you've done this on a fresh 2.6.32-358 install then that may not be your problem. If uname does show that you're using the supported kernel version and the path /lib/modules/2.6.32-358.el6.x86_64/build/ contains your headers you could try using the '-s' switch to give the build script the correct path for those.
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