diff --git a/apps/api/src/api/tool_instances.py b/apps/api/src/api/tool_instances.py
index 3e868d6..0dc0874 100644
--- a/apps/api/src/api/tool_instances.py
+++ b/apps/api/src/api/tool_instances.py
@@ -1341,11 +1341,25 @@ async def start_instance(
         manifest_def = await session.get(ToolDefinitionManifest, tool_type.manifest_id)
         if manifest_def:
             manifest = dict(manifest_def.manifest)
+            # Merge with base definition if referenced (user config is often in base)
+            if manifest_def.base_definition_id:
+                base_def = await session.get(
+                    ToolDefinitionManifest, manifest_def.base_definition_id
+                )
+                if base_def:
+                    manifest = resolve_base(deep_merge(dict(base_def.manifest), manifest))
             home_dir = get_manifest_home_dir(manifest)
             user_cfg = manifest.get("user")
             if user_cfg:
                 container_uid = user_cfg.get("uid", 0)
                 container_gid = user_cfg.get("gid", 0)
+            logger.debug(
+                "Manifest user resolved for instance %s: uid=%s, gid=%s, home=%s",
+                instance.id,
+                container_uid,
+                container_gid,
+                home_dir,
+            )
 
     # Apply selected config profile if any
     instance_dir = os.path.dirname(instance.compose_path)
diff --git a/apps/api/src/services/ssh_keys.py b/apps/api/src/services/ssh_keys.py
index c2ade84..2ab4c67 100644
--- a/apps/api/src/services/ssh_keys.py
+++ b/apps/api/src/services/ssh_keys.py
@@ -1,5 +1,6 @@
 """SSH key service utilities for preparing keys for container use."""
 
+import logging
 import os
 from pathlib import Path
 
@@ -7,6 +8,8 @@ from cryptography.fernet import Fernet
 
 from src.config import Settings
 
+logger = logging.getLogger(__name__)
+
 
 def _get_fernet() -> Fernet:
     """Generate a valid Fernet key from the session secret."""
@@ -75,10 +78,20 @@ def prepare_ssh_key_files(
             os.chown(private_key_path, effective_uid, effective_gid)
             os.chown(public_key_path, effective_uid, effective_gid)
             os.chown(config_path, effective_uid, effective_gid)
-        except PermissionError:
-            # API process may not be running as root; permission fixer will
-            # handle this post-start if the mount is read-write
-            pass
+            logger.debug(
+                "Set SSH key ownership to uid=%s gid=%s for %s",
+                effective_uid,
+                effective_gid,
+                ssh_dir,
+            )
+        except PermissionError as exc:
+            logger.warning(
+                "Cannot chown SSH keys to uid=%s gid=%s (running as uid=%s): %s",
+                effective_uid,
+                effective_gid,
+                os.getuid(),
+                exc,
+            )
 
     return str(ssh_dir)
 
diff --git a/apps/api/tests/unit/test_ssh_keys.py b/apps/api/tests/unit/test_ssh_keys.py
index 426fb4d..c659adf 100644
--- a/apps/api/tests/unit/test_ssh_keys.py
+++ b/apps/api/tests/unit/test_ssh_keys.py
@@ -13,7 +13,9 @@ class TestPrepareSshKeyFiles:
     """Tests for prepare_ssh_key_files."""
 
     @patch("src.services.ssh_keys._get_fernet")
-    def test_creates_files_with_default_permissions(self, mock_fernet, tmp_path) -> None:
+    def test_creates_files_with_default_permissions(
+        self, mock_fernet, tmp_path
+    ) -> None:
         mock_fernet.return_value.decrypt.return_value = b"private-key-content"
         ssh_key = MagicMock()
         ssh_key.private_key_encrypted = "enc"
@@ -35,9 +37,7 @@ class TestPrepareSshKeyFiles:
         ssh_key.public_key = "ssh-ed25519 AAA test@test"
 
         with patch("os.chown") as mock_chown:
-            ssh_dir = prepare_ssh_key_files(
-                str(tmp_path), ssh_key, uid=1001, gid=1001
-            )
+            ssh_dir = prepare_ssh_key_files(str(tmp_path), ssh_key, uid=1001, gid=1001)
 
         # os.chown is called for the directory and each of the 3 files
         assert mock_chown.call_count == 4
@@ -56,8 +56,6 @@ class TestPrepareSshKeyFiles:
 
         with patch("os.chown", side_effect=PermissionError("not allowed")):
             # Should not raise
-            ssh_dir = prepare_ssh_key_files(
-                str(tmp_path), ssh_key, uid=1001, gid=1001
-            )
+            ssh_dir = prepare_ssh_key_files(str(tmp_path), ssh_key, uid=1001, gid=1001)
 
         assert Path(ssh_dir).exists()