diff --git a/lib/spack/spack/modules/common.py b/lib/spack/spack/modules/common.py
index 66fe145f358..b5e084bc0c6 100644
--- a/lib/spack/spack/modules/common.py
+++ b/lib/spack/spack/modules/common.py
@@ -703,7 +703,7 @@ def configure_options(self):
 
         if os.path.exists(pkg.install_configure_args_path):
             with open(pkg.install_configure_args_path, "r") as args_file:
-                return args_file.read()
+                return spack.util.path.padding_filter(args_file.read())
 
         # Returning a false-like value makes the default templates skip
         # the configure option section
diff --git a/lib/spack/spack/util/path.py b/lib/spack/spack/util/path.py
index 124e8efec61..f894f6f3d8f 100644
--- a/lib/spack/spack/util/path.py
+++ b/lib/spack/spack/util/path.py
@@ -444,7 +444,7 @@ def padding_filter(string):
             r"(/{pad})+"  # the padding string repeated one or more times
             r"(/{longest_prefix})?(?=/)"  # trailing prefix of padding as path component
         )
-        regex = regex.replace("/", os.sep)
+        regex = regex.replace("/", re.escape(os.sep))
         regex = regex.format(pad=pad, longest_prefix=longest_prefix)
         _filter_re = re.compile(regex)