diff --git a/agent/skill_utils.py b/agent/skill_utils.py
index a302c6981a4..c901ee30d9d 100644
--- a/agent/skill_utils.py
+++ b/agent/skill_utils.py
@@ -471,7 +471,7 @@ def _normalize_string_set(values) -> Set[str]:
 # which becomes the dominant cost of ``hermes`` startup when ~120 skills
 # each trigger a category lookup during banner construction (10+ seconds
 # of pure waste).
-_EXTERNAL_DIRS_CACHE: Dict[Tuple[str, int], List[Path]] = {}
+_EXTERNAL_DIRS_CACHE: Dict[Tuple[str, int, int], List[Path]] = {}
 
 
 def _external_dirs_cache_clear() -> None:
@@ -496,11 +496,13 @@ def get_external_skills_dirs() -> List[Path]:
     if not config_path.exists():
         return []
 
-    # Cache key: (absolute path, mtime_ns).  stat() is ~2us vs ~85ms for
-    # the full YAML parse, so the fast path is nearly free.
+    # Cache key: (absolute path, mtime_ns, size).  stat() is ~2us vs ~85ms
+    # for the full YAML parse, so the fast path is nearly free.  Size is in
+    # the key because overlayfs (CI runner pods) can coalesce rapid writes
+    # into a single mtime_ns tick.
     try:
         stat = config_path.stat()
-        cache_key: Tuple[str, int] = (str(config_path), stat.st_mtime_ns)
+        cache_key: Tuple[str, int, int] = (str(config_path), stat.st_mtime_ns, stat.st_size)
     except OSError:
         cache_key = None  # type: ignore[assignment]
 
diff --git a/gateway/run.py b/gateway/run.py
index 911021a36ee..6bad574f3ef 100644
--- a/gateway/run.py
+++ b/gateway/run.py
@@ -21427,7 +21427,7 @@ class GatewayRunner(GatewayAuthorizationMixin, GatewayKanbanWatchersMixin, Gatew
         "honcho.runtime_peer_prefix",
         "honcho.user_peer_aliases",
     )
-    _HONCHO_CACHE_BUSTING_MEMO: dict[tuple[str, int | None], dict[str, Any]] = {}
+    _HONCHO_CACHE_BUSTING_MEMO: dict[tuple[str, tuple[int, int] | None], dict[str, Any]] = {}
 
     @classmethod
     def _empty_honcho_cache_busting_config(cls) -> dict[str, Any]:
@@ -21441,10 +21441,14 @@ class GatewayRunner(GatewayAuthorizationMixin, GatewayKanbanWatchersMixin, Gatew
 
             path = resolve_config_path()
             try:
-                mtime_ns = path.stat().st_mtime_ns
+                st = path.stat()
+                # mtime alone is not enough: overlayfs (CI runner pods)
+                # coalesces rapid writes into one mtime_ns tick. Size joins
+                # the key so a same-tick content change still re-parses.
+                stat_sig = (st.st_mtime_ns, st.st_size)
             except OSError:
-                mtime_ns = None
-            memo_key = (str(path), mtime_ns)
+                stat_sig = None
+            memo_key = (str(path), stat_sig)
             cached = cls._HONCHO_CACHE_BUSTING_MEMO.get(memo_key)
             if cached is not None:
                 return dict(cached)