3.1.1 and 3.2.1 are running my i5-3350P at 80% CPU. 3 GPUs (7850, 7950, 6970). Eventually locks up the machine, solid. Was OK with 2.11.4. Running 7x64 with 12.8 drivers.
That's driver and sdk related, nothing to do with cgminer - it caches bin files generated the first time you run it and will run the same ever more on that cgminer even if you change drivers, so you almost certainly changed drivers between cgminer versions.