When I upgraded from Premiere Pro and AME CS5.5 to 2014.1 CC all my encodes were not utilising the 6 cores of my i7 980 Gulftown processor.
Previous version CS5.5 worked perfectly but 2014.1CC didn't So edited the registry to ensure the system wouldn't park the CPU's as per the details here
UltimateComputers.net Forum - View topic - Disable Core Parking Windows 7 Tweak may improve performance from the post of MMeguro25-Jun-2014.
Then I noticed the issue now appeared to me a little intermittent. After a little more searching around for me the final fix was to ensure that "Import Sequences Natively" was disabled in the Adobe Media Encoder preferences.
I am still running 2014.1 CC and have not yet updated to 2014.2 CC as looking at the release notes there does not seem to be any fixes/features which will either help in gerneral or fix the issue within the applications.
http://blogs.adobe.com/premierepro/2014/12/premiere-pro-cc-2014-2-release.html
Adobe Media Encoder CC (2014.2) Update | Premiere Pro work area