Sorry for the belated reply here.
I'm not very familiar with IsolatedConnection, so rockot@ might be able to comment more. If you want to investigate more yourself, I would add a disconnect handler and start tracing backwards to see where the disconnection is coming from.
If you want to have multiple message pipes going over this IsolatedConnection, bootstrapping it with some broker interface that vends other interfaces (e.g. like the InterfaceProvider solution linked above) sounds right to me.
Daniel