diff --git a/pylabrobot/liquid_handling/backends/simulation/simulation_tests.py b/pylabrobot/liquid_handling/backends/simulation/simulation_tests.py
index b584246a2c..7f3aec68e0 100644
--- a/pylabrobot/liquid_handling/backends/simulation/simulation_tests.py
+++ b/pylabrobot/liquid_handling/backends/simulation/simulation_tests.py
@@ -64,7 +64,7 @@ def test_get_index_html(self):
     """ Test that the index.html file is returned. """
     r = requests.get("http://localhost:1337/", timeout=10)
     self.assertEqual(r.status_code, 200)
-    self.assertEqual(r.headers["Content-Type"], "text/html")
+    self.assertIn(r.headers["Content-Type"], ["text/html", "text/html; charset=utf-8"])
 
   async def test_connect(self):
     await self.client.send('{"event": "ready"}')
diff --git a/pylabrobot/liquid_handling/backends/simulation/simulator_backend.py b/pylabrobot/liquid_handling/backends/simulation/simulator_backend.py
index af450cb5ab..a364e96e14 100644
--- a/pylabrobot/liquid_handling/backends/simulation/simulator_backend.py
+++ b/pylabrobot/liquid_handling/backends/simulation/simulator_backend.py
@@ -42,7 +42,7 @@ class SimulatorBackend(WebSocketBackend):
     >>> from pylabrobot.liquid_handling.liquid_handler import LiquidHandler
     >>> sb = simulation.SimulatorBackend()
     >>> lh = LiquidHandler(backend=sb)
-    >>> lh.setup()
+    >>> await lh.setup()
     INFO:websockets.server:server listening on 127.0.0.1:2121
     INFO:pyhamilton.liquid_handling.backends.simulation.simulation:Simulation server started at
       http://127.0.0.1:2121
@@ -127,11 +127,11 @@ def _run_file_server(self):
 
     def start_server():
       # try to start the server. If the port is in use, try with another port until it succeeds.
-      og_path = os.getcwd()
-      os.chdir(path) # only within thread.
-
       class QuietSimpleHTTPRequestHandler(http.server.SimpleHTTPRequestHandler):
         """ A simple HTTP request handler that does not log requests. """
+        def __init__(self, *args, **kwargs):
+          super().__init__(*args, directory=path, **kwargs)
+
         def log_message(self, format, *args):
           # pylint: disable=redefined-builtin
           pass
@@ -148,8 +148,6 @@ def log_message(self, format, *args):
 
       self.httpd.serve_forever()
 
-      os.chdir(og_path)
-
     self._fst = threading.Thread(name="simulation_fs", target=start_server, daemon=True)
     self.fst.start()
 
diff --git a/pylabrobot/liquid_handling/backends/websocket.py b/pylabrobot/liquid_handling/backends/websocket.py
index e55c9043a5..9035ce1a0f 100644
--- a/pylabrobot/liquid_handling/backends/websocket.py
+++ b/pylabrobot/liquid_handling/backends/websocket.py
@@ -266,7 +266,7 @@ def start_loop():
     lock = threading.Lock()
     lock.acquire() # pylint: disable=consider-using-with
     self._loop = asyncio.new_event_loop()
-    self._t = threading.Thread(target=start_loop)
+    self._t = threading.Thread(target=start_loop, daemon=True)
     self.t.start()
 
     while lock.locked():
diff --git a/pylabrobot/liquid_handling/liquid_handler.py b/pylabrobot/liquid_handling/liquid_handler.py
index 3db24fb28f..bfe50211ea 100644
--- a/pylabrobot/liquid_handling/liquid_handler.py
+++ b/pylabrobot/liquid_handling/liquid_handler.py
@@ -95,7 +95,7 @@ async def setup(self):
     for resource in self.deck.children:
       self.resource_assigned_callback(resource)
 
-    super().setup()
+    await super().setup()
 
   def update_head_state(self, state: Dict[int, Optional[Tip]]):
     """ Update the state of the liquid handler head.
diff --git a/pylabrobot/machine.py b/pylabrobot/machine.py
index bd354392b6..8001215a0c 100644
--- a/pylabrobot/machine.py
+++ b/pylabrobot/machine.py
@@ -46,8 +46,10 @@ def setup_finished(self) -> bool:
     return self._setup_finished
 
   async def setup(self):
-    self.backend.setup()
+    await self.backend.setup()
+    self._setup_finished = True
 
   @need_setup_finished
   async def stop(self):
-    self.backend.stop()
+    await self.backend.stop()
+    self._setup_finished = False
diff --git a/pylabrobot/server/liquid_handling_api_tests.py b/pylabrobot/server/liquid_handling_api_tests.py
index 180c00313b..7ce64155af 100644
--- a/pylabrobot/server/liquid_handling_api_tests.py
+++ b/pylabrobot/server/liquid_handling_api_tests.py
@@ -1,3 +1,4 @@
+import time
 from typing import cast
 import unittest
 
@@ -53,6 +54,7 @@ def test_setup(self): # TODO: Figure out how we can configure LH
 
       self.assertIn(response.json.get("status"), {"running", "succeeded"})
 
+      time.sleep(0.1)
       assert self.lh.setup_finished
 
   def test_stop(self):
@@ -111,6 +113,7 @@ def setUp(self) -> None:
       assert self.lh.deck.resources == deck.resources
 
     client.post(self.base_url + "/setup")
+    time.sleep(0.5)
 
   def test_tip_pickup(self):
     with self.app.test_client() as client:
@@ -125,7 +128,6 @@ def test_tip_pickup(self):
           "tip": serialize(tip),
           "offset": None,
         }], "use_channels": [0]})
-      print(response)
       self.assertIn(response.json.get("status"), {"running", "succeeded"})
       self.assertEqual(response.status_code, 200)