Nope, playing as Flauros. I did have a Mage guild, and I was able to upgrade the first Archmage with no problems in the same city. Oh, and I may have given the 3 mages vampirism before I tried to upgrade, I know I didn't for the Archmage.
Did you happen to lose Reagents between the time the first Mage was upgraded and the time you tried to upgrade the rest?