diff --git a/lib/galaxy/config/__init__.py b/lib/galaxy/config/__init__.py
index 5cae18bf10bd..8e4ce9ca23ff 100644
--- a/lib/galaxy/config/__init__.py
+++ b/lib/galaxy/config/__init__.py
@@ -301,7 +301,7 @@ def is_set(self, key):
         # To check only schema options, change the line below to `if property not in self._raw_config:`
         if key not in self._raw_config:
             log.warning(f"Configuration option does not exist: '{key}'")
-        return key in self._kwargs
+        return key in self._kwargs and self._kwargs[key]
 
     def resolve_path(self, path):
         """Resolve a path relative to Galaxy's root."""
@@ -511,10 +511,10 @@ def resolve(key):
             if not parent:  # base case: nothing else needs resolving
                 return path
             parent_path = resolve(parent)  # recursively resolve parent path
-            if path is not None:
+            if path:
                 path = os.path.join(parent_path, path)  # resolve path
             else:
-                path = parent_path  # or use parent path
+                log.warning("Trying to resolve path for the '%s' option but it's empty/None", key)
 
             setattr(self, key, path)  # update property
             _cache[key] = path  # cache it!