Have you checked in the repsonse tab that it isn't running the job as a response to the alert being raised ?

I had this problem where through Management Studio I could not remove the tick from the box on "run job" in the response tab, so was getting spammed by alert emails as I ran the job, the alert was raised, which then ran the job agaiin, which alerted etc etc.

Whatever I did, restarting the agent etc I could not get my removal of the tick box to stick.

So finally I scripted the alert to a new window, deleted the original, and modiied the script to remove all job refs before running it to recreate the alert. Bingo ! The alert was created with the job part geyed out and box not ticked. Am now very happy that it will do what I want.