diff --git a/openflexure_microscope/config.py b/openflexure_microscope/config.py
index 062e66b0..c5d6edad 100644
--- a/openflexure_microscope/config.py
+++ b/openflexure_microscope/config.py
@@ -60,7 +60,7 @@ def json_map(data, clean_keys=True):
     """
 
     # Do not overwrite original data dictionary
-    d = copy.copy(data)
+    d = copy.deepcopy(data)
 
     # If we're cleaning up unsuitable keys
     if clean_keys:
diff --git a/openflexure_microscope/microscope.py b/openflexure_microscope/microscope.py
index f18d68dd..5f01a51b 100644
--- a/openflexure_microscope/microscope.py
+++ b/openflexure_microscope/microscope.py
@@ -231,14 +231,14 @@ class Microscope(object):
 
         return self.rc.read(json_safe=json_safe)
 
-    def save_config(self):
+    def save_config(self, backup: bool = True):
         """
         Saves the current runtime-config back to disk
         """
         # Get any changed device settings
-        self.read_config()
+        self.read_config(json_safe=False)
         # Save to disk
-        self.rc.save()
+        self.rc.save(backup=backup)
 
     @property
     def config(self) -> dict: