Blizzard has announced that they are aware of an issue in Cataclysm Classic that is causing players’ Guild Reputation to reset to Neutral. They are currently working on a fix for this issue but do not yet have an estimate of when it will be corrected.
Cataclysm Classic Phase 4 Overview Guide
I logged in to my Shaman on Cata classic (this character), finished my JC daily and noticed my guild reputation increased despite being exalted since I finished leveling near launch.
