In Things you SHOULD know about Diablo 2 you will find your answer in bullet 14 (
http://www.battle.net/forums/thread.aspx?fn=d2-gameplay&t=163465&p=1&#post163465):
Upgrading items does not guarantee higher stats. All it does is take a normal base item to exceptional status, or an exceptional item to elite status. The end stats depend on the stats of the upgraded base item.
Vampire Gaze is probably the most famous example.
Grim helms have a defense range of 60-125. All Vampire Gaze Grim Helms have a defense of 252. This is due to the fact that when armors spawn with the enhanced defense mod, the defense is invariably set at max +1. When we are dealing with a Vampire Gaze, the base item's defense of 126 recieves a 100% bonus = 252 defense.
However, when the item is upgraded, the base defense is rerolled. The defense range of Bone Visages is 100-157. Which means that a Vampire Gaze with a base item defense of 126 has a very good chance of being turned into a Bone Visage with a lower defense. In case of the worst roll imaginable, your 252 defense Vampire Gaze would go down to 200. Not good.
This page shows how upgrading will affect the various unique items.
http://www.cs.colostate.edu/~deykea/d2armours.html