Interestingly enough, this is actually authentic behavior and is working as intended. When the Isle progresses to a certain point via daily quest completions, the weather will begin to improve.
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Weather on Isle of Quel’Danas Tied to Progression on Burning Crusade Classic
Blizzard has shared some insight regarding the weather effects on the Isle of Quel'Danas, explaining that rain is tied to progress in the Battle for Sun's Reach.