The clock speed goes down when you use more cores. When you use only six cores, both 6 core and 12 core run at the same clock speed. With 8 or 12 cores used, the clock speed goes down. Intel tells you the speed when _all_ cores are used, so 6 core machine running at 3.5GHz with six cores is advertised as 3.5 GHz, but a 12 core machine running at 3.5GHz with six cores and 2.7GHz with 12 cores is advertised as 2.7GHz.
In reality, the 12 core machine has 30 MB of cache memory which makes it faster than the 6 core machine with only 15 MB cache, if the same number of cores are used.
Your figures are off, but the general idea is accurate. The 12 core processor is never as fast as the others no matter how many cores are used, and the 6 core has 12MB of cache instead of 15.