Maybe I don't understand all of the mechanics, but I'm wondering why my toon (Steinbran, US-Gorgonnash) has a rating of 2893 while our main tank (Mt, US-Gorgonnash) has a rating of 2930.
Our gear score difference (using the "compare" tool) only has a difference of 13 points. We are both fully enchanted (135) and are both only using all epic gems. The only thing I can think of is that he has 4 more gem slots total on his gear. But this seems silly. Since (especially in ToC) for a given ilvl there is really only one item for each class per slot. In addition, two of these slots are from blacksmithing skill, so if there's a bonus from them it seems unfair that my tailoring/enchanting doesn't add to my score.
When dealing with top available gear such as you and your guildie have, some minor differences (2930 - 2893 = 37, it's around 1% difference in gear) may occur, especially when comparing 2 opposite classes/roles.