The clock on a CPU is actually an external crystal, but usually runs at about 100MHz. Inside the CPU, this clock is multiplied by some constant to produce a sig

The clock on a CPU is actually an external crystal, but usually runs at about 100MHz. Inside the CPU, this clock is multiplied by some constant to produce a signal in the GHz range (using a phase-locked or delay-locked loop). Then the clock is distributed across the die with a large number of buffers called a clock tree. I suspect the measured skew comes from those on-die components that can't easily be placed outside the package.