Are you using the latest version of the RadarBox software - RadarBox 2009?
Also, if you set the alert criteria when those aircraft are already in the list, you won't get an alarm. For example, no alerts set but 43C123 is in the list. You set the alarm and nothing will happen. However, when 43C124 appears, the alarm will sound. Also, the next time you pick up 43C123 you will get an alert.
In my experience, the alert function works 100% and I use it a lot.
Make sure you don't have any "blank" characters after the entries in the alert setup lists.