I have "2" teirs of specilization. One to scan Old BC items, and one to scan new WotLK items. The problem was instead of looking at ItemLevel to determine what expansion i was looking at, i had it set to look at ItemScore, which was always 0 at that time. Oops! So many of you may notice a boost in GearScore.
On the other hand, The loss of gems/enchants will drop everyone on average 7%. So I have changed the exponential slider to compensate for this. Scores should change very little now.