If the checkboxes are in the html, the JavaScript should be able to access them. You say that the first alert appears which means it is being called.
What does nested mean? Is it using frames/iframes?
I do not code MooTools, I just know the basics from using it a long time ago, but I would expect the code to look more like this
Basic idea
I used named functions instead out of habit.
Examples
Like you way with name
http://jsfiddle.net/5hPbV/
Using a class instead of a name
http://jsfiddle.net/5hPbV/1/
Eric