diff --git a/builder/src/windows.ts b/builder/src/windows.ts
index 6781652..5718356 100644
--- a/builder/src/windows.ts
+++ b/builder/src/windows.ts
@@ -78,7 +78,9 @@ import site
   await fixPipRegistryIssue(path.join(pyBinRoot, 'Lib', 'site-packages', 'pip'));
 
   // Install rest of the packages required in all environments
-  await util.runCommand(pythonExe, ['-m', 'pip', 'install', 'virtualenv', 'wheel']);
+  // Pin virtualenv: 21.2.4 breaks the virtualenv->venv copy trick on embedded Python
+  // (venv creation silently fails with non-zero exit code).
+  await util.runCommand(pythonExe, ['-m', 'pip', 'install', 'virtualenv==21.2.1', 'wheel']);
 
   // We have to patch pip embedded into venv package:
   const venvEmbeddedWheelsDir = path.join(pyBinRoot, 'Lib', 'site-packages', 'virtualenv', 'seed', 'wheels', 'embed');
diff --git a/checker/whitelists/python-3.12.10-h5ad/windows-x64.json b/checker/whitelists/python-3.12.10-h5ad/windows-x64.json
index d6d5b4b..0511d14 100644
--- a/checker/whitelists/python-3.12.10-h5ad/windows-x64.json
+++ b/checker/whitelists/python-3.12.10-h5ad/windows-x64.json
@@ -1,7 +1,4 @@
 {
-  "charset_normalizer-3.*.whl": {
-    "81d243bd2c585b0f4821__mypyc": "invalid decimal literal"
-  },
   "matplotlib-3.*-cp312-cp312-win_amd64.whl": {
     "matplotlib._c_internal_utils": "Could not determine home directory",
     "matplotlib._image": "Could not determine home directory",
@@ -16,7 +13,6 @@
     "numba.np.ufunc.tbbpool": "DLL load failed while importing tbbpool: The specified module could not be found"
   },
   "scipy-1.*-win_amd64.whl": {
-    "scipy.linalg._matfuncs_sqrtm_triu": "cannot import name 'within_block_loop' from partially initialized module",
-    "scipy.stats._unuran.unuran_wrapper": "module 'numpy.random.bit_generator' has no attribute 'SeedlessSequence'"
+    "scipy.linalg._matfuncs_sqrtm_triu": "cannot import name 'within_block_loop' from partially initialized module"
   }
 }
diff --git a/checker/whitelists/python-3.12.10-rapids/windows-x64.json b/checker/whitelists/python-3.12.10-rapids/windows-x64.json
index 56148d9..a214f4a 100644
--- a/checker/whitelists/python-3.12.10-rapids/windows-x64.json
+++ b/checker/whitelists/python-3.12.10-rapids/windows-x64.json
@@ -1,16 +1,9 @@
 {
-  "charset_normalizer-3.*.whl": {
-    "81d243bd2c585b0f4821__mypyc": "invalid decimal literal"
-  },
   "numba-0.*-win_amd64.whl": {
     "numba.np.ufunc.tbbpool": "DLL load failed while importing tbbpool: The specified module could not be found"
   },
   "scipy-1.*-win_amd64.whl": {
-    "scipy.linalg._matfuncs_sqrtm_triu": "cannot import name 'within_block_loop' from partially initialized module",
-    "scipy.stats._unuran.unuran_wrapper": "module 'numpy.random.bit_generator' has no attribute 'SeedlessSequence'"
-  },
-  "rpy2_rinterface-3.*.whl": {
-    "_rinterface_cffi_api": "DLL load failed while importing _rinterface_cffi_api: The specified module could not be found."
+    "scipy.linalg._matfuncs_sqrtm_triu": "cannot import name 'within_block_loop' from partially initialized module"
   },
   "torch-2.7.0+cpu-cp312-cp312-win_amd64.whl": {
     "functorch._C": "initialization failed"
diff --git a/checker/whitelists/python-3.12.10-sccoda/windows-x64.json b/checker/whitelists/python-3.12.10-sccoda/windows-x64.json
index 1284759..95876ef 100644
--- a/checker/whitelists/python-3.12.10-sccoda/windows-x64.json
+++ b/checker/whitelists/python-3.12.10-sccoda/windows-x64.json
@@ -1,4 +1,7 @@
 {
+  "charset_normalizer-3.*.whl": {
+    "81d243bd2c585b0f4821__mypyc": "invalid decimal literal"
+  },
   "matplotlib-3.*-cp312-cp312-win_amd64.whl": {
     "matplotlib._c_internal_utils": "Could not determine home directory",
     "matplotlib._image": "Could not determine home directory",
@@ -18,14 +21,7 @@
   "rpy2_rinterface-3.*.whl": {
     "_rinterface_cffi_api": "DLL load failed while importing _rinterface_cffi_api: The specified module could not be found"
   },
-  "charset_normalizer-3.*.whl": {
-    "81d243bd2c585b0f4821__mypyc": "invalid decimal literal"
-  },
   "scipy-1.*-win_amd64.whl": {
-    "scipy.linalg._matfuncs_sqrtm_triu": "cannot import name 'within_block_loop' from partially initialized module",
-    "scipy.stats._unuran.unuran_wrapper": "module 'numpy.random.bit_generator' has no attribute 'SeedlessSequence'"
-  },
-  "tensorflow-2.*.whl": {
-    "tensorflow.lite.python._pywrap_tensorflow_lite_metrics_wrapper": "generic_type: type \"MetricsWrapper\" is already registered"
+    "scipy.linalg._matfuncs_sqrtm_triu": "cannot import name 'within_block_loop' from partially initialized module"
   }
 }
diff --git a/checker/whitelists/python-3.12.10/windows-x64.json b/checker/whitelists/python-3.12.10/windows-x64.json
index 178197c..86960a2 100644
--- a/checker/whitelists/python-3.12.10/windows-x64.json
+++ b/checker/whitelists/python-3.12.10/windows-x64.json
@@ -1,5 +1,8 @@
 {
-  "matplotlib-3.*-win_amd64.whl": {
+  "charset_normalizer-3.*.whl": {
+    "81d243bd2c585b0f4821__mypyc": "invalid decimal literal"
+  },
+  "matplotlib-3.*-cp312-cp312-win_amd64.whl": {
     "matplotlib._c_internal_utils": "Could not determine home directory",
     "matplotlib._image": "Could not determine home directory",
     "matplotlib._path": "Could not determine home directory",
@@ -15,22 +18,12 @@
   "rpy2_rinterface-3.*.whl": {
     "_rinterface_cffi_api": "DLL load failed while importing _rinterface_cffi_api: The specified module could not be found"
   },
-  "charset_normalizer-3.*.whl": {
-    "81d243bd2c585b0f4821__mypyc": "invalid decimal literal"
-  },
   "scipy-1.*-win_amd64.whl": {
-    "scipy.linalg._matfuncs_sqrtm_triu": "cannot import name 'within_block_loop' from partially initialized module",
-    "scipy.stats._unuran.unuran_wrapper": "module 'numpy.random.bit_generator' has no attribute 'SeedlessSequence'"
+    "scipy.linalg._matfuncs_sqrtm_triu": "cannot import name 'within_block_loop' from partially initialized module"
   },
   "torch-2.7.0+cpu-cp312-cp312-win_amd64.whl": {
     "functorch._C": "initialization failed"
   },
-  "torch-2.9.1+cpu-cp312-cp312-win_amd64.whl": {
-    "functorch._C": "initialization failed"
-  },
-  "tensorflow-2.*.whl": {
-    "tensorflow.lite.python._pywrap_tensorflow_lite_metrics_wrapper": "generic_type: type \"MetricsWrapper\" is already registered"
-  },
   "torchaudio-2.7.0+cpu-cp312-cp312-win_amd64.whl": {
     "torio.lib._torio_ffmpeg4": "DLL load failed while importing _torio_ffmpeg4: The specified module could not be found",
     "torio.lib._torio_ffmpeg5": "DLL load failed while importing _torio_ffmpeg5: The specified module could not be found",