Full Text Index And Mail Agent

We have a few mail in databases with new mail notification agents that worked fine until recently. We received an error in the log stating we needed to create a full text index in order for the mail notification agent to run. We created the indexes but on SOME of the db’s the agent triggered a mail notification on old documents, yet worked correctly in other db’s by only triggering a notification on new mail which is what he should have done. Any ideas? We basically just told the users to delete the unnecessary notifications but it would be nice to find an answer on this. Thanks!