If the XML document loaded by the configuration contains a string property with multiple values (separated by the list delimiter character), on saving, this property is split into multiple nodes. So
This also happens if the property is not touched before saving. The reason for this behavior is that on loading new nodes are created for the single list items (which is required to have an internal model on which queries can be executed). On saving, these nodes are considered new nodes, and thus new XML elements are created for them.