We would first of all recommend that you update your current installation to version 6.0.0.42 as there have been changes made to the E-mail alerts system. You can update by following the steps in
this knowledge base article.
Once you have updated your installation check that you have correctly setup your Time schedules for the reports. You can checked these under Deployment\Scheduled Deployments. Check that the schedule that you are using for those reports is not repeating itself multiple times a day.