One thing to keep in mind when comparing PCMark Vantage results is that the benchmark's margin of error is fairly wide—we'd estimate 5-7 percent. Relevant factors include whether or not the hard drive was defragmented immediately prior to the run and whether Vantage was run immediately following OS+driver installation, or only after a full suite of tests and other benchmarks had been run.
We used the 64-bit version of the benchmark and defragmented the hard drive immediately prior to running it. However, since the Origin PC used an Intel SSD instead of a standard hard drive, we avoided defragging the drive in favor of using Intel's TRIM utility.
The Shift scorched through PCMark Vantage to such a degree that we re-ran the test several times on both systems to make sure our scores hadn't been glitched. Part of the performance difference between the two systems is because the Shift has more available cores, a potentially faster SSD, and a higher clockspeed, but part of it may be AHCI (Advanced Host Controller Interface).
Origin Genesis: Core i7 920 @ 3.8GHz, Maingear Shift: Core i7 980X @ 4.2GHz
Most systems and motherboards, including Origin's Genesis, ship with their storage controllers set for IDE mode. In some cases, this makes sense—IDE mode doubles as a legacy compatibility mode, and some SATA controllers, including those made by JMicron and AMD, actually perform better in that mode. The problem with disabling AHCI is that it prevents the drive from using features like NCQ or hot-swapping. MainGear's SHIFT ships with AHCI enabled, and we're guessing that accounts for at least a chunk of the 6000+ gap in scores.