diff --git a/bootstrap.bat b/bootstrap.bat
index e8840745a6d33..7ec6c608da9c8 100644
--- a/bootstrap.bat
+++ b/bootstrap.bat
@@ -2,7 +2,7 @@
 ::
 :: Automatically generated by `create_entry_points.py`; DO NOT EDIT.
 ::
-:: To make modifications to this file, edit `tools/run_python.bat` and then run
+:: To make modifications to this file, edit `tools/maint/run_python.bat` and then run
 :: `tools/maint/create_entry_points.py`
 
 :: N.b. In Windows .bat scripts, the ':' character cannot appear inside any if () blocks,
@@ -26,7 +26,7 @@
   set "MYDIR=%~dp0"
   goto FOUND_MYDIR
 )
-@for %%I in (%~n0.bat) do (
+@for %%I in (%~n0.bat) do @(
   @if exist %%~$PATH:I (
     set MYDIR=%%~dp$PATH:I
   ) else (
diff --git a/em++.bat b/em++.bat
index 7b690151414fc..2c771aee30a15 100644
--- a/em++.bat
+++ b/em++.bat
@@ -2,8 +2,8 @@
 ::
 :: Automatically generated by `create_entry_points.py`; DO NOT EDIT.
 ::
-:: To make modifications to this file, edit `tools/run_python_compiler.bat` and
-:: then run `tools/create_entry_points.py`
+:: To make modifications to this file, edit `tools/maint/run_python_compiler.bat` and
+:: then run `tools/maint/create_entry_points.py`
 
 :: N.b. In Windows .bat scripts, the ':' character cannot appear inside any if () blocks,
 :: or there will be a parsing error.
@@ -26,7 +26,7 @@
   set "MYDIR=%~dp0"
   goto FOUND_MYDIR
 )
-@for %%I in (%~n0.bat) do (
+@for %%I in (%~n0.bat) do @(
   @if exist %%~$PATH:I (
     set MYDIR=%%~dp$PATH:I
   ) else (
diff --git a/emcc.bat b/emcc.bat
index 7b690151414fc..2c771aee30a15 100644
--- a/emcc.bat
+++ b/emcc.bat
@@ -2,8 +2,8 @@
 ::
 :: Automatically generated by `create_entry_points.py`; DO NOT EDIT.
 ::
-:: To make modifications to this file, edit `tools/run_python_compiler.bat` and
-:: then run `tools/create_entry_points.py`
+:: To make modifications to this file, edit `tools/maint/run_python_compiler.bat` and
+:: then run `tools/maint/create_entry_points.py`
 
 :: N.b. In Windows .bat scripts, the ':' character cannot appear inside any if () blocks,
 :: or there will be a parsing error.
@@ -26,7 +26,7 @@
   set "MYDIR=%~dp0"
   goto FOUND_MYDIR
 )
-@for %%I in (%~n0.bat) do (
+@for %%I in (%~n0.bat) do @(
   @if exist %%~$PATH:I (
     set MYDIR=%%~dp$PATH:I
   ) else (
diff --git a/test/runner.bat b/test/runner.bat
index e8840745a6d33..7ec6c608da9c8 100644
--- a/test/runner.bat
+++ b/test/runner.bat
@@ -2,7 +2,7 @@
 ::
 :: Automatically generated by `create_entry_points.py`; DO NOT EDIT.
 ::
-:: To make modifications to this file, edit `tools/run_python.bat` and then run
+:: To make modifications to this file, edit `tools/maint/run_python.bat` and then run
 :: `tools/maint/create_entry_points.py`
 
 :: N.b. In Windows .bat scripts, the ':' character cannot appear inside any if () blocks,
@@ -26,7 +26,7 @@
   set "MYDIR=%~dp0"
   goto FOUND_MYDIR
 )
-@for %%I in (%~n0.bat) do (
+@for %%I in (%~n0.bat) do @(
   @if exist %%~$PATH:I (
     set MYDIR=%%~dp$PATH:I
   ) else (
diff --git a/test/test_other.py b/test/test_other.py
index 5a510607b098a..71aac29aff83d 100644
--- a/test/test_other.py
+++ b/test/test_other.py
@@ -15102,11 +15102,7 @@ def test_shell_cmd_with_quotes(self):
     print('running cmd:', cmd)
     with env_modify({'PATH': new_path}):
       proc = subprocess.run(cmd, capture_output=True, text=True, shell=True, check=True)
-      # There is currently a bug in the windows .bat files that leads to stdout
-      # not being empty in this case.
-      # See https://github.com/emscripten-core/emscripten/pull/25416
-      if not WINDOWS:
-        self.assertEqual(proc.stdout, '')
+      self.assertEqual(proc.stdout, '')
       self.assertEqual(proc.stderr, '')
 
   def test_browser_too_old(self):
diff --git a/tools/maint/run_python.bat b/tools/maint/run_python.bat
index e8840745a6d33..7ec6c608da9c8 100644
--- a/tools/maint/run_python.bat
+++ b/tools/maint/run_python.bat
@@ -2,7 +2,7 @@
 ::
 :: Automatically generated by `create_entry_points.py`; DO NOT EDIT.
 ::
-:: To make modifications to this file, edit `tools/run_python.bat` and then run
+:: To make modifications to this file, edit `tools/maint/run_python.bat` and then run
 :: `tools/maint/create_entry_points.py`
 
 :: N.b. In Windows .bat scripts, the ':' character cannot appear inside any if () blocks,
@@ -26,7 +26,7 @@
   set "MYDIR=%~dp0"
   goto FOUND_MYDIR
 )
-@for %%I in (%~n0.bat) do (
+@for %%I in (%~n0.bat) do @(
   @if exist %%~$PATH:I (
     set MYDIR=%%~dp$PATH:I
   ) else (
diff --git a/tools/maint/run_python_compiler.bat b/tools/maint/run_python_compiler.bat
index 7b690151414fc..2c771aee30a15 100644
--- a/tools/maint/run_python_compiler.bat
+++ b/tools/maint/run_python_compiler.bat
@@ -2,8 +2,8 @@
 ::
 :: Automatically generated by `create_entry_points.py`; DO NOT EDIT.
 ::
-:: To make modifications to this file, edit `tools/run_python_compiler.bat` and
-:: then run `tools/create_entry_points.py`
+:: To make modifications to this file, edit `tools/maint/run_python_compiler.bat` and
+:: then run `tools/maint/create_entry_points.py`
 
 :: N.b. In Windows .bat scripts, the ':' character cannot appear inside any if () blocks,
 :: or there will be a parsing error.
@@ -26,7 +26,7 @@
   set "MYDIR=%~dp0"
   goto FOUND_MYDIR
 )
-@for %%I in (%~n0.bat) do (
+@for %%I in (%~n0.bat) do @(
   @if exist %%~$PATH:I (
     set MYDIR=%%~dp$PATH:I
   ) else (