I'm not sure why you're getting that problem. When you say on your PC, as a out-of-browser app, or just downloading the source and using that directly?
The way I would structure it is to have something similar as the charting controls in Silverlight Toolkit (http://timheuer.com/blog/archive/2008/10/28/silverlight-toolkit-released-with-charting-databinding.aspx) were you have Series and you can add multiple
series. So something like BarSeries, and you add a series for each Z position and you specify either the Z position or you automatically calculate it.
Each series would then be databound to a collection of data items.
Basically, create an abstraction that uses NodesControl for each series and InstancingNodes for the bars itself. The InstancingNodes uses a template and this you provide a UserControl that you create yourself and override a property called DataItem - in
the DataItem override you can change your nodes inside the UserControl, set the scale in your case, as well as the position.
Have a look at the InstancingNodes sample for how to use that specifically.
I'm not sure how I can explain this further - without writing the entire code.. :)