Damn I suspected as much! This is code I was using to edit, the code I used to create it is below. Basically I check to see if the file exists and if not I run the create then edit, if it does then I run just the previous edit sub. Thanks for the reply, I will look into XPath and let you know how I go :-)
Public Sub CreateSettingsFile()
Dim stmWriter As New IsolatedStorageFileStream("PlanningGDBToolsSettings.xml", FileMode.Create, m_pIsoStorage)
Dim writer As New Xml.XmlTextWriter(stmWriter, Encoding.UTF8)
Try
writer.Formatting = Xml.Formatting.Indented
writer.WriteStartDocument()
writer.WriteStartElement("UserSettings")
writer.WriteStartElement("WorkingMXD")
writer.WriteString("Some mxd")
writer.WriteEndElement()
writer.WriteStartElement("Test1")
writer.WriteString("Test unsuccessful")
writer.WriteEndElement()
writer.WriteEndElement()
Catch ex As Exception
MsgBox("CreateSettingsFile - " & ex.Message)
Finally
writer.Flush()
writer.Close()
stmWriter.Close()
End Try
End Sub