diff --git a/src/openflexure_microscope_server/utilities.py b/src/openflexure_microscope_server/utilities.py
index 2f6c90a4..a13cf19d 100644
--- a/src/openflexure_microscope_server/utilities.py
+++ b/src/openflexure_microscope_server/utilities.py
@@ -164,7 +164,9 @@ def make_path_safe(unsafe_path_string: str) -> str:
             else:
                 sanitised = unsafe_character_pattern.sub("_", sanitised)
 
-            sanitised_components.append(_sanitise_reserved(sanitised))
+            sanitised_components.append(
+                _sanitise_reserved(sanitised, is_filename=False)
+            )
         else:
             sanitised_components.append(component)
 
@@ -194,20 +196,26 @@ def make_name_safe(unsafe_name_string: str) -> str:
     return _sanitise_reserved(name)
 
 
-def _sanitise_reserved(name: str) -> str:
+def _sanitise_reserved(name: str, is_filename: bool = True) -> str:
     """Check a name against Windows reserved names.
 
     :param name: The component to check.
-    :returns: The sanitised component.
+    :param is_filename: Whether the component is a filename.
+    If True, names will be forced into lowercase.
+    :returns: The sanitised component, in lower case.
     """
     # Check for Windows reserved names.
     # These are reserved even with an extension (e.g. NUL.txt).
     # We check the part before the first dot.
     base_name = name.split(".", maxsplit=1)[0].upper()
     if base_name in _WINDOWS_RESERVED_NAMES:
-        return f"{name}_"
+        return f"{name.lower()}_" if is_filename else f"{name}_"
 
-    return name
+    # We force names to be lowercase to avoid issues on
+    # Windows where files with the same name
+    # but different case can cause problems when checking if
+    # a file already exists.
+    return name.lower() if is_filename else name
 
 
 class VersionData(BaseModel):
diff --git a/tests/unit_tests/test_scan_directories.py b/tests/unit_tests/test_scan_directories.py
index 603587a3..80121a32 100644
--- a/tests/unit_tests/test_scan_directories.py
+++ b/tests/unit_tests/test_scan_directories.py
@@ -247,6 +247,36 @@ def test_scan_sequence_and_listing(caplog):
         assert len(caplog.records) == 0
 
 
+def test_scan_sequence_case_sensitive():
+    """Check created scans are added in order and listed correctly, even when cases are different."""
+    _clear_scan_dir()
+    scan_dir_manager = ScanDirectoryManager(BASE_SCAN_DIR)
+
+    # Create some scan data and mark it as successful to get an end date.
+    scan_data = fake_active_scan_data()
+    scan_data.set_final_data(result="Success")
+    # Make 4 scans
+    scan_dir = scan_dir_manager.new_scan_dir("fake_scan")
+    scan_dir.save_scan_data(scan_data)
+    scan_dir = scan_dir_manager.new_scan_dir("FAKE_SCAN")
+    scan_dir.save_scan_data(scan_data)
+    scan_dir = scan_dir_manager.new_scan_dir("Fake_Scan")
+    scan_dir.save_scan_data(scan_data)
+    scan_dir = scan_dir_manager.new_scan_dir("FAKE_scan")
+    scan_dir.save_scan_data(scan_data)
+    scan_dir = scan_dir_manager.new_scan_dir("fAkE_sCaN")
+    scan_dir.save_scan_data(scan_data)
+
+    # Check they exist and are numbered sequentially
+    all_scans = scan_dir_manager.all_scans
+    assert_unique_of_length(all_scans, 5)
+    assert "fake_scan_0001" in all_scans
+    assert "fake_scan_0002" in all_scans
+    assert "fake_scan_0003" in all_scans
+    assert "fake_scan_0004" in all_scans
+    assert "fake_scan_0005" in all_scans
+
+
 def test_scan_name_non_sequential():
     """Check new scan has the correct name if the directories are not sequential."""
     _clear_scan_dir()
diff --git a/tests/unit_tests/test_utilities.py b/tests/unit_tests/test_utilities.py
index 52b94fad..dbff78e4 100644
--- a/tests/unit_tests/test_utilities.py
+++ b/tests/unit_tests/test_utilities.py
@@ -17,6 +17,7 @@ def test_make_name_safe_basic():
     assert make_name_safe("name with spaces") == "name_with_spaces"
     assert make_name_safe("name/with/slashes") == "name_with_slashes"
     assert make_name_safe("name\\with\\backslashes") == "name_with_backslashes"
+    assert make_name_safe("sPoNgEmoCk") == "spongemock"
 
 
 def test_make_name_safe_trailing_chars():
@@ -34,21 +35,25 @@ def test_make_name_safe_trailing_chars():
 def test_make_name_safe_reserved_names(name):
     """Test Windows reserved names."""
     # Base name should be sanitized
-    assert make_name_safe(name) == f"{name}_"
+    assert make_name_safe(name) == f"{name.lower()}_"
     # Case-insensitive
     assert make_name_safe(name.lower()) == f"{name.lower()}_"
     # With extension
-    assert make_name_safe(f"{name}.txt") == f"{name}.txt_"
+    assert make_name_safe(f"{name}.txt") == f"{name.lower()}.txt_"
     # Multiple extensions
-    assert make_name_safe(f"{name}.tar.gz") == f"{name}.tar.gz_"
+    assert make_name_safe(f"{name}.tar.gz") == f"{name.lower()}.tar.gz_"
 
 
 def test_make_name_safe_reserved_names_false_positives():
     """Test that names containing but not equal to reserved names are safe."""
-    assert make_name_safe("CONSTANT") == "CONSTANT"
-    assert make_name_safe("CON2") == "CON2"
-    assert make_name_safe("ICON") == "ICON"
-    assert make_name_safe("CHILLI CON CARNE") == "CHILLI_CON_CARNE"
+    assert make_name_safe("CONSTANT") == "constant"
+    assert make_name_safe("CON2") == "con2"
+    assert make_name_safe("ICON") == "icon"
+    assert make_name_safe("icon") == "icon"
+    assert make_name_safe("iCon") == "icon"
+    assert make_name_safe("iCOn") == "icon"
+    assert make_name_safe("icOn") == "icon"
+    assert make_name_safe("CHILLI CON CARNE") == "chilli_con_carne"
 
 
 def test_make_path_safe_basic():