The first difference that we can really measure in performance is memory bandwidth. Both Sandra and WinRAR indicate that MSI has slightly less aggressive sub timings in order to ensure system stability and compatibility. In day to day operations you would not notice this very slight difference in performance. Note that the Gigabyte board had the memory timings set to "Xtreme" in its sub menu which would give it this slight advantage.
I was very surprised to see that the render time in Cinebench was actually 1 second faster on the MSI P55-GD65.
In 3D Gaming performance, the two systems again perform identically.
Finally, in PC Mark Vantage, the MSI P55-GD65 trades blows with the Gigabyte P55-UD6 in the various tests, with neither really outperforming the other overall.