diff --git a/server/src/config/mod.rs b/server/src/config/mod.rs
index d3ea29ec..78627ef3 100644
--- a/server/src/config/mod.rs
+++ b/server/src/config/mod.rs
@@ -246,7 +246,13 @@ fn default_max_mesh_peers() -> usize {
 }
 
 /// Configuration for a project component (name, path, setup/teardown commands).
+///
+/// `deny_unknown_fields` turns a top-level setting that lands inside a
+/// `[[component]]` table (e.g. because it was placed below the last
+/// `[[component]]` header) into a hard parse error instead of a silently
+/// dropped key.
 #[derive(Debug, Clone, Deserialize)]
+#[serde(deny_unknown_fields)]
 #[allow(dead_code)]
 pub struct ComponentConfig {
     pub name: String,
diff --git a/server/src/config/tests.rs b/server/src/config/tests.rs
index a614fee6..ce1252c0 100644
--- a/server/src/config/tests.rs
+++ b/server/src/config/tests.rs
@@ -521,6 +521,26 @@ runtime = "openai"
     assert!(err.contains("unknown runtime 'openai'"));
 }
 
+#[test]
+fn unrecognized_key_in_component_table_errors_instead_of_silently_dropping() {
+    // Regression for story 1177: a top-level setting that ends up attached to
+    // a `[[component]]` table (e.g. because it was placed below the last
+    // `[[component]]` header) must be a hard error, not a silently swallowed
+    // key.
+    let toml_str = r#"
+[[component]]
+name = "server"
+path = "."
+base_branch = "main"
+"#;
+
+    let err = ProjectConfig::parse(toml_str).unwrap_err();
+    assert!(
+        err.contains("base_branch"),
+        "expected error to mention the unrecognized key, got: {err}"
+    );
+}
+
 // ── base_branch config ──────────────────────────────────────────────────
 
 #[test]
diff --git a/server/src/io/fs/scaffold/helpers.rs b/server/src/io/fs/scaffold/helpers.rs
index df2b0ab2..32a01a0b 100644
--- a/server/src/io/fs/scaffold/helpers.rs
+++ b/server/src/io/fs/scaffold/helpers.rs
@@ -8,8 +8,13 @@ use super::detect::detect_components_toml;
 use super::templates::{DEFAULT_AGENTS_TOML, DEFAULT_PROJECT_SETTINGS_TOML};
 
 pub(super) fn generate_project_toml(root: &Path) -> String {
+    // TOML requires bare `key = value` settings to appear before any table
+    // header. Emitting components (which open with `[[component]]`) first
+    // would make every commented top-level setting below them silently
+    // attach to the last `[[component]]` table once uncommented, instead of
+    // the top-level document — so settings must come first.
     let components = detect_components_toml(root);
-    format!("{components}\n{DEFAULT_PROJECT_SETTINGS_TOML}")
+    format!("{DEFAULT_PROJECT_SETTINGS_TOML}\n{components}")
 }
 
 pub(super) fn write_file_if_missing(path: &Path, content: &str) -> Result<(), String> {
diff --git a/server/src/io/fs/scaffold/tests.rs b/server/src/io/fs/scaffold/tests.rs
index 42e7b76b..b0aa63a6 100644
--- a/server/src/io/fs/scaffold/tests.rs
+++ b/server/src/io/fs/scaffold/tests.rs
@@ -140,6 +140,38 @@ fn scaffold_project_toml_round_trips_through_project_config_load() {
     );
 }
 
+#[test]
+fn scaffold_project_toml_uncommenting_base_branch_takes_effect() {
+    use crate::config::ProjectConfig;
+
+    // Regression for story 1177: the scaffold template used to emit
+    // `[[component]]` headers before the commented top-level settings, so
+    // uncommenting a setting like `base_branch` attached it to the last
+    // `[[component]]` table instead of the top level, silently no-opping.
+    let dir = tempdir().unwrap();
+    fs::write(
+        dir.path().join("Cargo.toml"),
+        "[package]\nname = \"myapp\"\n",
+    )
+    .unwrap();
+    scaffold_story_kit(dir.path(), 3001).unwrap();
+
+    let content = fs::read_to_string(dir.path().join(".huskies/project.toml")).unwrap();
+    assert!(
+        content.contains("# base_branch = \"main\""),
+        "scaffold should emit a commented-out base_branch line to uncomment"
+    );
+    let uncommented = content.replace("# base_branch = \"main\"", "base_branch = \"main\"");
+
+    let config =
+        ProjectConfig::parse(&uncommented).expect("uncommented project.toml should still parse");
+    assert_eq!(
+        config.base_branch,
+        Some("main".to_string()),
+        "uncommenting base_branch in the scaffolded project.toml must take effect"
+    );
+}
+
 #[test]
 fn scaffold_context_is_blank_template_not_story_kit_content() {
     let dir = tempdir().unwrap();