Try opening Advanced Alert Manager with "Run as Administrator". I've found that occasionally the alert manager cannot see the custom properties unless you do this.
An optional extension of this alert idea is to create some custom properties such as AlertEmailAddress1 and AlertEmailAddress2, and put the primary email address into the first custom property. In your alert, instead of typing in the email address in the To field, you can put ${Nodes.AlertEmailAddress1};${Nodes.AlertEmailAddress2}. The system will fill in the primary email as well as the second email address (if you have one). This way you only need the single node down alert.
Alert Central would solve these issues as well. Use a filter in Alert Central to feed the alerts to the appropriate department.