If you aren't validating then you don't need access to the schemas. If you are validating, and you don't have access to them, then validation will fail -- and it sounds like that didn't happen. So I think the schema business is a red herring.
Also the first thing you need to know about namespaces is that it's the namespace URI which defines the namespace, not the prefix. When you try to match a namespaced element, you have to match the namespace URI of the namespace, not the prefix.
So... is the namespace of the root element equal to the namespace which you are using to search for other elements? I'm assuming that JDOM's Namespace object has an equals() method which tells you that.