diff --git a/demo/clean.sh b/demo/clean.sh
index c5dabd4767..418ca9457e 100755
--- a/demo/clean.sh
+++ b/demo/clean.sh
@@ -11,7 +11,9 @@ if [ -f $PID_FILE ]; then
     exit 1
 fi
 
-find "$DIR" -name "*.log" -delete
-find "$DIR" -name "*.db" -delete
+for port in 8080 8081 8082; do
+    rm -rf $DIR/$port
+    rm -rf $DIR/media_store.$port
+done
 
 rm -rf $DIR/etc
diff --git a/demo/start.sh b/demo/start.sh
index b9cc14b9d2..b5dea5e176 100755
--- a/demo/start.sh
+++ b/demo/start.sh
@@ -8,14 +8,6 @@ cd "$DIR/.."
 
 mkdir -p demo/etc
 
-# Check the --no-rate-limit param
-PARAMS=""
-if [ $# -eq 1 ]; then
-    if [ $1 = "--no-rate-limit" ]; then
-	    PARAMS="--rc-messages-per-second 1000 --rc-message-burst-count 1000"
-    fi
-fi
-
 export PYTHONPATH=$(readlink -f $(pwd))
 
 
@@ -35,6 +27,15 @@ for port in 8080 8081 8082; do
         -H "localhost:$https_port" \
         --config-path "$DIR/etc/$port.config" \
 
+    # Check script parameters
+    if [ $# -eq 1 ]; then
+        if [ $1 = "--no-rate-limit" ]; then
+            # Set high limits in config file to disable rate limiting
+            perl -p -i -e 's/rc_messages_per_second.*/rc_messages_per_second: 1000/g' $DIR/etc/$port.config
+            perl -p -i -e 's/rc_message_burst_count.*/rc_message_burst_count: 1000/g' $DIR/etc/$port.config
+        fi
+    fi
+
     python -m synapse.app.homeserver \
         --config-path "$DIR/etc/$port.config" \
         -D \
diff --git a/synapse/config/_base.py b/synapse/config/_base.py
index c408db2b4a..73f6959959 100644
--- a/synapse/config/_base.py
+++ b/synapse/config/_base.py
@@ -149,6 +149,8 @@ class Config(object):
         )
         config_args, remaining_args = config_parser.parse_known_args(argv)
 
+        generate_keys = config_args.generate_keys
+
         if config_args.generate_config:
             if not config_args.config_path:
                 config_parser.error(
@@ -156,51 +158,40 @@ class Config(object):
                     " generated using \"--generate-config -H SERVER_NAME"
                     " -c CONFIG-FILE\""
                 )
-
-            config_dir_path = os.path.dirname(config_args.config_path[0])
-            config_dir_path = os.path.abspath(config_dir_path)
-
-            server_name = config_args.server_name
-            if not server_name:
-                print "Must specify a server_name to a generate config for."
-                sys.exit(1)
             (config_path,) = config_args.config_path
-            if not os.path.exists(config_dir_path):
-                os.makedirs(config_dir_path)
-            if os.path.exists(config_path):
-                print "Config file %r already exists" % (config_path,)
-                yaml_config = cls.read_config_file(config_path)
-                yaml_name = yaml_config["server_name"]
-                if server_name != yaml_name:
-                    print (
-                        "Config file %r has a different server_name: "
-                        " %r != %r" % (config_path, server_name, yaml_name)
-                    )
+            if not os.path.exists(config_path):
+                config_dir_path = os.path.dirname(config_path)
+                config_dir_path = os.path.abspath(config_dir_path)
+
+                server_name = config_args.server_name
+                if not server_name:
+                    print "Must specify a server_name to a generate config for."
                     sys.exit(1)
-                config_bytes, config = obj.generate_config(
-                    config_dir_path, server_name
-                )
-                config.update(yaml_config)
-                print "Generating any missing keys for %r" % (server_name,)
-                obj.invoke_all("generate_files", config)
-                sys.exit(0)
-            with open(config_path, "wb") as config_file:
-                config_bytes, config = obj.generate_config(
-                    config_dir_path, server_name
-                )
-                obj.invoke_all("generate_files", config)
-                config_file.write(config_bytes)
+                if not os.path.exists(config_dir_path):
+                    os.makedirs(config_dir_path)
+                with open(config_path, "wb") as config_file:
+                    config_bytes, config = obj.generate_config(
+                        config_dir_path, server_name
+                    )
+                    obj.invoke_all("generate_files", config)
+                    config_file.write(config_bytes)
                 print (
-                    "A config file has been generated in %s for server name"
-                    " '%s' with corresponding SSL keys and self-signed"
-                    " certificates. Please review this file and customise it to"
-                    " your needs."
+                    "A config file has been generated in %r for server name"
+                    " %r with corresponding SSL keys and self-signed"
+                    " certificates. Please review this file and customise it"
+                    " to your needs."
                 ) % (config_path, server_name)
-            print (
-                "If this server name is incorrect, you will need to regenerate"
-                " the SSL certificates"
-            )
-            sys.exit(0)
+                print (
+                    "If this server name is incorrect, you will need to"
+                    " regenerate the SSL certificates"
+                )
+                sys.exit(0)
+            else:
+                print (
+                    "Config file %r already exists. Generating any missing key"
+                    " files."
+                ) % (config_path,)
+                generate_keys = True
 
         parser = argparse.ArgumentParser(
             parents=[config_parser],
@@ -218,7 +209,7 @@ class Config(object):
                 " -c CONFIG-FILE\""
             )
 
-        config_dir_path = os.path.dirname(config_args.config_path[0])
+        config_dir_path = os.path.dirname(config_args.config_path[-1])
         config_dir_path = os.path.abspath(config_dir_path)
 
         specified_config = {}
@@ -231,12 +222,12 @@ class Config(object):
         config.pop("log_config")
         config.update(specified_config)
 
+        if generate_keys:
+            obj.invoke_all("generate_files", config)
+            sys.exit(0)
+
         obj.invoke_all("read_config", config)
 
         obj.invoke_all("read_arguments", args)
 
-        if config_args.generate_keys:
-            obj.invoke_all("generate_files", config)
-            sys.exit(0)
-
         return obj