Pressing CTRL and sneaking makes one more stealthy than walking/running, even with Silence perk.

What am I missing, what does Silence perk actually do?

I was testing this today with load/save and while I could sneak by the door without problem and just stand there.. I could not do the same just walking/running with Silence perk. Without crouching I was instantly detected.

When you're sneaking, the speed at wich you're moving determines your chances to be caught. That perk simply makes It as if you were standing still while sneaking even if you move (ONLY takes effect while sneaking).