Which versions of Windows are you running on each PC?
I recently had a performance issue where 2 PCs with EXACT same HW specifications ran a highly parallel .NET application at drastically different speeds.
The "fast" PC was running Windows 7.
The "slow" PC was running Windows Server 2012.
The Windows Server 2012 PC would never get CPU utilization over 30% for the application run while the Windows 7 PC would run the application with 85-90% CPU utilization. So the Windows Server 2012 would take 2.5 hours to run what the Windows 7 PC did in ~1 hour.
The PROBLEM with the Windows Server 2012 PC was that it had "Balanced" Power Options set.
Once this was set to "Performance" option it ran as fast as the Windows 7 PC. This setting doesn't seem to make a difference on Windows 7 though.
This fixed it here:
http://support.microsoft.com/kb/2207548[
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