OK, that's a little freaky. We haven't used basic alerts for quite some time, but we didn't have this issue in the past.
Is there any chance you could migrate to advanced alerts instead? They are much more versatile, and the ability to link them to custom properties can greatly simplify alert management. Also, the use of custom SQL queries in email alerts allows much more useful information to be passed with the email messages.
It might be a good idea to start moving in that direction, as they are likely to be phased out at some point.