diff --git a/crates/skills/src/commands.rs b/crates/skills/src/commands.rs
index 5cf4b3acd..ae6eb10d0 100644
--- a/crates/skills/src/commands.rs
+++ b/crates/skills/src/commands.rs
@@ -140,12 +140,16 @@ fn locale_compare(a: &str, b: &str) -> std::cmp::Ordering {
 fn check(io: &mut Io) -> R<()> {
     let (sys, _) = ctx(io);
     let root = sys.find_project_root();
-    // Prefer the user-level tree when one exists so leftover project-layout
-    // dirs cannot make a current install look stale (#824). Stay on inferred
-    // scope otherwise so a home-rooted project install (`install -y`) is
-    // still visible.
-    let scope = if sys.is_home_dir(&root) && sys.is_already_installed(&root, Some(Scope::User)).is_some() {
-        Some(Scope::User)
+    // A home-rooted tree is either the user-level install or a project
+    // install under ~. Pick one scope so leftover dirs on the other layout
+    // cannot make a current copy look stale (#824). Inferred scope walks
+    // both, which is what produced the false "Updates available".
+    let scope = if sys.is_home_dir(&root) {
+        if sys.is_already_installed(&root, Some(Scope::User)).is_some() {
+            Some(Scope::User)
+        } else {
+            Some(Scope::Project)
+        }
     } else {
         None
     };
diff --git a/crates/skills/tests/drift_ports_tests.rs b/crates/skills/tests/drift_ports_tests.rs
index 4d37efd87..b00b6c526 100644
--- a/crates/skills/tests/drift_ports_tests.rs
+++ b/crates/skills/tests/drift_ports_tests.rs
@@ -547,10 +547,15 @@ fn check_sees_home_rooted_project_scope_pi_install() {
     assert_eq!(r.code, 0, "{}\n{}", r.stdout, r.stderr);
     assert!(std::path::Path::new(&format!("{home}/.pi/skills/impeccable/SKILL.md")).exists());
     assert!(!std::path::Path::new(&format!("{home}/.pi/agent/skills/impeccable/SKILL.md")).exists());
+    write(
+        &format!("{home}/.pi/agent/skills/other/SKILL.md"),
+        "---\nname: other\n---\nLeftover user-layout skill.\n",
+    );
 
     let r = run_cli(&["check"], &home, &env);
     assert!(!r.stdout.contains("not installed"), "{}\n{}", r.stdout, r.stderr);
     assert!(r.stdout.contains("Skills are up to date"), "{}\n{}", r.stdout, r.stderr);
+    assert!(!r.stdout.contains("Updates available"), "{}", r.stdout);
     std::fs::remove_dir_all(&root).ok();
 }