I'm honestly not sure what is wrong. I've scoured the code looking for typos and what not, or maybe some weird null reference. One thing that is really odd is that I can access the variables within the class, like, if I did print(boxes[0].contents);, I would see 1.0.

One major note is that this isn't the actual function, I was just using this to get my point across.

Try just that, it works for me

#pragma strict

public class BacASableJS extends MonoBehaviour 
{
	public class Box
	{
	    public var contents : float = 1.0;
	    function GetContents(){ return(contents); }
	}	
	
	public var boxes : Box[] = new Box[10]; //10 is arbitrary
	
	function Start()
	{
		for(var i = 0; i < boxes.length; i++)
			boxes[i] = new Box();
	}
	
	/*function Update()
	{
	    for(var i = 0; i < boxes.length; i++)
	    {
	        var tmpBox : Box = boxes[i];
	        print(tmpBox.GetContents());
	    }
	}*/


	function Update()
	{
	    for(var i = 0; i < boxes.length; i++)
	    {
	        var tmpBox : Box = boxes[i];
	        print("getting the contents now..."); //added this line
	        print(tmpBox.GetContents());
	        print("you should see contents"); //and this one
	    }
	}	
}