That's Very Strange.
Maybe the second processor is further from the power supply so the electricity takes longer to get to and from it.
Oh ok, seriously then.
Is there any diagnostic stuff you can run on them?
Or, maybe the memory serving the CPUs isn't shared, and the half serving the slow one is faulty? Could it be a dodgy memory stick?
I know you don't really 'do' hardware but maybe swap them around and run it again.
The only other thing I can think might help is to reset the BIOS to its "optimised defaults" in case a setting's gone squiffy.
Failing that you could always bring it to ComputerFIX (discount for cat owners).