Sorry it took so long to get back. I tried it and it didn't work BUT the solution seems to be to use the NAMESPACE command. When you reference a scene into a scene, a namespace is assigned to everything in the referenced scene. By default, the referenced scene name is used as the namespace however, you can change it to whatever you want.

The easy answer is to include the name of your scene into any mel scripts that you write that will be used with the referenced scene. That way the script will be looking for the proper name.

The more complex answer would be to assign a variable as the namespace in the mel script then assign a name to it that matches the namespace of the referenced scene. By doing this, you could reference the same scene multiple times then include a short script to swap the namespace variable so that you could use the same Mel script to control all of the referenced scenes. This would be good in cases where you design a single character but want to use copies of it in a scene. By assigning a different namespace to each copy of the referenced scene and changing the namespace variable in the mel scripts you don't need a seperate script for each reference. ZoinK!