The differences between the plots are negligible; probably not statistically significant.
Also, with DVI, the video card really plays no role in profiling, since communication between the card and monitor is all digital. The monitor is the only significant part. With VGA, you're profiling not only the analog response of the monitor to input signal voltages, but the analog response of the video card to various input values going into the DAC chip and coming out the jack on the back of the card. A VGA profile is only good for a specific video card - monitor pair, while a DVI profile is good for the monitor, no matter what card it is connected to.