diff --git a/wrolpi/cmd.py b/wrolpi/cmd.py
index b5317396..76895932 100644
--- a/wrolpi/cmd.py
+++ b/wrolpi/cmd.py
@@ -299,7 +299,8 @@ async def run_command(cmd: tuple[str | pathlib.Path, ...], cwd: pathlib.Path | s
                 await proc.wait()
 
             if reader_task:
-                reader_task.cancel()
+                # Drain remaining stdout.  Cancelling here races the last lines on a fast process
+                # (CI often loses "line three" because wait() returns before the reader finishes).
                 try:
                     await reader_task
                 except (CancelledError, asyncio.CancelledError):
diff --git a/wrolpi/common.py b/wrolpi/common.py
index 7769567c..acfe2999 100644
--- a/wrolpi/common.py
+++ b/wrolpi/common.py
@@ -2382,23 +2382,24 @@ def chunks_by_stem(it: List[Union[pathlib.Path, str, int]], size: int) -> Genera
     from wrolpi.files.lib import split_path_stem_and_suffix
     it = sorted(it.copy())
     index = size
-    last_stem = None
+    last_key = None
     while it:
         if index >= len(it):
             # Ran out of items, yield what is left.
             yield it
             return
         path = it[index]
+        path = pathlib.Path(path)
         stem, _ = split_path_stem_and_suffix(path)
-        if last_stem and stem != last_stem:
-            # Found a break in the path names, yield and reset.
+        key = (str(path.parent), stem)
+        if last_key and key != last_key:
+            # Found a break in directory or stem, yield and reset.
             chunk, it = it[:index], it[index:]
             index = size
-            last_stem = None
+            last_key = None
             yield chunk
             continue
-        # Didn't find a name change, try again.
-        last_stem = stem
+        last_key = key
         index += 1
 
 
diff --git a/wrolpi/files/lib.py b/wrolpi/files/lib.py
index a9c6cbf9..ce034a14 100644
--- a/wrolpi/files/lib.py
+++ b/wrolpi/files/lib.py
@@ -1500,16 +1500,16 @@ def group_files_by_stem(files: List[pathlib.Path], pre_sorted: bool = False) ->
     files = sorted(files) if not pre_sorted else files.copy()
     file = files.pop(0)
     group = [file, ]
-    prev_stem, _ = split_path_stem_and_suffix(file)
+    prev_dir, prev_stem = file.parent, split_path_stem_and_suffix(file)[0]
     for file in files:
-        stem, suffix = split_path_stem_and_suffix(file)
-        if stem == prev_stem:
+        stem, _ = split_path_stem_and_suffix(file)
+        if stem == prev_stem and file.parent == prev_dir:
             group.append(file)
             continue
-        # Stem has changed, group is finished.
+        # Directory or stem changed, group is finished.
         yield group
         group = [file, ]
-        prev_stem = stem
+        prev_dir, prev_stem = file.parent, stem
     yield group
 
 
diff --git a/wrolpi/files/test/test_lib.py b/wrolpi/files/test/test_lib.py
index a6cfc230..95f29d1d 100644
--- a/wrolpi/files/test/test_lib.py
+++ b/wrolpi/files/test/test_lib.py
@@ -930,6 +930,13 @@ def test_group_files_by_stem(make_files_structure, test_directory):
          test_directory / 'foo.txt'],
     ]
 
+    make_files_structure(['dir_a/s3.bin', 'dir_b/s3.bin'])
+    same_stem = [test_directory / 'dir_a/s3.bin', test_directory / 'dir_b/s3.bin']
+    assert list(lib.group_files_by_stem(same_stem)) == [
+        [test_directory / 'dir_a/s3.bin'],
+        [test_directory / 'dir_b/s3.bin'],
+    ]
+
 
 def test_get_primary_file(test_directory, video_file, srt_file3, example_epub, example_mobi, example_pdf,
                           singlefile_contents_factory, make_files_structure):