diff --git a/lib/config/index.js b/lib/config/index.js
index fae51e5..cc71564 100644
--- a/lib/config/index.js
+++ b/lib/config/index.js
@@ -110,8 +110,8 @@ for (let i = keys.length; i--;) {
   // and the config with uppercase is not set
   // we set the new config using the old key.
   if (uppercase.test(keys[i]) &&
-  config[lowercaseKey] &&
-  !config[keys[1]]) {
+  config[lowercaseKey] !== undefined &&
+  fileConfig[keys[i]] === undefined) {
     logger.warn('config.js contains deprecated lowercase setting for ' + keys[i] + '. Please change your config.js file to replace ' + lowercaseKey + ' with ' + keys[i])
     config[keys[i]] = config[lowercaseKey]
   }