diff --git a/red/nodes/Flow.js b/red/nodes/Flow.js
index 8eea60831..4f56b0daf 100644
--- a/red/nodes/Flow.js
+++ b/red/nodes/Flow.js
@@ -301,7 +301,6 @@ Flow.prototype.start = function() {
     if (this.missingTypes.length > 0) {
         throw new Error("missing types");
     }
-    
     events.emit("nodes-starting");
 
     for (var id in this.nodes) {
@@ -435,7 +434,13 @@ Flow.prototype.applyConfig = function(config,type) {
     }
         
     var flow = this;
+    if (type != "full") {
+        log.info("Stopping modified "+type);
+    }
     return this.stop(activeNodesToStop).then(function() {
+        if (type != "full") {
+            log.info("Stopped modified "+type);
+        }
         flow.parseConfig(config);
         for (var i=0;i<nodesToRewire.length;i++) {
             var node = flow.activeNodes[nodesToRewire[i]];
@@ -443,7 +448,13 @@ Flow.prototype.applyConfig = function(config,type) {
                 node.updateWires(flow.allNodes[node.id].wires);
             }
         }
+        if (type != "full") {
+            log.info("Starting modified "+type);
+        }
         flow.start();
+        if (type != "full") {
+            log.info("Started modified "+type);
+        }
     })
 }
 
diff --git a/red/nodes/credentials.js b/red/nodes/credentials.js
index a9353a164..df815bb2f 100644
--- a/red/nodes/credentials.js
+++ b/red/nodes/credentials.js
@@ -190,6 +190,7 @@ module.exports = {
                 }
             }
             credentialCache[nodeID] = savedCredentials;
+            delete node.credentials;
         }
     },
     
diff --git a/red/nodes/flows.js b/red/nodes/flows.js
index 55fce9072..e34b1c8b3 100644
--- a/red/nodes/flows.js
+++ b/red/nodes/flows.js
@@ -75,45 +75,6 @@ var flowNodes = module.exports = {
         activeFlow.eachNode(cb);
     },
     
-    /**
-     * Stops all active nodes and clears the active set
-     * @return a promise for the stopping of all active nodes
-     */
-    //clear: function(nodesToStop) {
-    //    var stopList;
-    //    if (nodesToStop == null) {
-    //        stopList = Object.keys(nodes);
-    //    } else {
-    //        stopList = Object.keys(nodesToStop);
-    //    }
-    //    console.log(stopList);
-    //    return when.promise(function(resolve) {
-    //        events.emit("nodes-stopping");
-    //        var promises = [];
-    //        console.log("running nodes:",Object.keys(nodes).length);
-    //        for (var i=0;i<stopList.length;i++) {
-    //            var node = nodes[stopList[i]];
-    //            if (node) {
-    //                try {
-    //                    var p = node.close();
-    //                    if (p) {
-    //                        promises.push(p);
-    //                    }
-    //                } catch(err) {
-    //                    node.error(err);
-    //                }
-    //                delete nodes[stopList[i]];
-    //                delete activeConfigNodes[stopList[i]];
-    //            }
-    //        }
-    //        console.log("running nodes:",Object.keys(nodes).length);
-    //        when.settle(promises).then(function() {
-    //            events.emit("nodes-stopped");
-    //            resolve();
-    //        });
-    //    });
-    //},
-
     /**
      * @return the active configuration
      */
@@ -135,7 +96,12 @@ var flowNodes = module.exports = {
         
         var credentialSavePromise = null;
         
-        config.forEach(function(node) {
+        
+        // Clone config and extract credentials prior to saving
+        // Original config needs to retain credentials so that flow.applyConfig
+        // knows which nodes have had changes.
+        var cleanConfig = clone(config);
+        cleanConfig.forEach(function(node) {
             if (node.credentials) {
                 credentials.extract(node);
                 credentialsChanged = true;
@@ -148,22 +114,22 @@ var flowNodes = module.exports = {
             credentialSavePromise = when.resolve();
         }
         
-        
         if (type=="full") {
             return credentialSavePromise
-                    .then(function() { return storage.saveFlows(config);})
-                    .then(function() { return flowNodes.stopFlows(); })
-                    .then(function() { activeFlow = new Flow(config); flowNodes.startFlows();});
+                .then(function() { return storage.saveFlows(cleanConfig);})
+                .then(function() { return flowNodes.stopFlows(); })
+                .then(function() { activeFlow = new Flow(config); flowNodes.startFlows();});
         } else {
             return credentialSavePromise
-                    .then(function() { return storage.saveFlows(config);})
-                    .then(function() { return activeFlow.applyConfig(config,type); });
+                .then(function() { return storage.saveFlows(cleanConfig);})
+                .then(function() { return activeFlow.applyConfig(config,type); });
         }
     },
     startFlows: function() {
         log.info("Starting flows");
         try {
             activeFlow.start();
+        log.info("Started flows");
         } catch(err) {
             var missingTypes = activeFlow.getMissingTypes();
             if (missingTypes.length > 0) {
@@ -177,7 +143,10 @@ var flowNodes = module.exports = {
     },
     stopFlows: function() {
         log.info("Stopping flows");
-        return activeFlow.stop();
+        return activeFlow.stop().then(function() {
+            log.info("Stopped flows");
+            return;
+        });
     }
 };