While its possible that you could have some distortion based on the port you use, you are much more likely to see a difference based on the natural variances of the monitors (remember that you are using consumer grade panels that have much wider range of what is considered "acceptable" vs a professional display). If you care about your monitors truly being matched, you should pick up a calibration unit (Like the SpyderPro) that will measure your monitors and create profiles to match them to standards. Then not only will they match each other, but you can also be assured they are outputting the "true" image.
Otherwise, assuming you're using a standard setup, there's no dramatic advantage of DisplayPort to DVI (again, assuming a standard setup where you're driving a pair of 1920x1200 displays connected via 6ft cables). A lot of the advantages of DisplayPort relate to higher bandwidth applications that you don't need to worry about with a 24" display.
And finally, remember that HDMI and DVI are electrically identical and use the same encoding (only difference is that HDMI includes audio) so you can actually drive 3 displays using the same "type" of port using that card (assuming you used both DVIs and the HDMI).