diff --git a/lib/bundler/settings.rb b/lib/bundler/settings.rb
index 1139eab503..8c69e81490 100644
--- a/lib/bundler/settings.rb
+++ b/lib/bundler/settings.rb
@@ -461,7 +461,7 @@ module Bundler
             new_k = k.gsub("-", "___")
           end
 
-          config[new_k] = v
+          config[new_k] = v.to_s
           config
         end
       end
diff --git a/lib/bundler/yaml_serializer.rb b/lib/bundler/yaml_serializer.rb
index 9e56a944bb..09e77ab449 100644
--- a/lib/bundler/yaml_serializer.rb
+++ b/lib/bundler/yaml_serializer.rb
@@ -58,7 +58,7 @@ module Bundler
       str.split(/\r?\n/).each do |line|
         if match = HASH_REGEX.match(line)
           indent, key, quote, val = match.captures
-          key = convert_to_backward_compatible_key(key) if key.match?(/__/)
+          key = convert_to_backward_compatible_key(key)
           key = key[1..-1].to_sym if key.start_with?(":")
           depth = indent.scan(/  /).length
           if quote.empty? && val.empty?
@@ -77,24 +77,9 @@ module Bundler
           last_hash[last_empty_key].push(convert_to_ruby_value(val))
         end
       end
-      deep_transform_values_with_empty_hash!(res)
       res
     end
 
-    def deep_transform_values_with_empty_hash!(hash)
-      hash.transform_values! do |v|
-        if v.is_a?(Hash)
-          if v.empty?
-            nil
-          else
-            deep_transform_values_with_empty_hash!(v)
-          end
-        else
-          v
-        end
-      end
-    end
-
     def convert_to_ruby_value(val)
       if val.match?(/\A:(.*)\Z/)
         val[1..-1].to_sym
@@ -102,8 +87,6 @@ module Bundler
         val.to_i
       elsif val.match?(/\Atrue|false\Z/)
         val == "true"
-      elsif val.empty?
-        nil
       else
         val
       end
diff --git a/lib/rubygems/config_file.rb b/lib/rubygems/config_file.rb
index 36cf20194c..97c11bd95d 100644
--- a/lib/rubygems/config_file.rb
+++ b/lib/rubygems/config_file.rb
@@ -352,7 +352,27 @@ if you believe they were disclosed to a third party.
 
     begin
       content = Bundler::YAMLSerializer.load(File.read(filename))
-      unless content.is_a? Hash
+      if content.is_a? Hash
+        content.transform_keys! do |k|
+          if k.match?(/__/)
+            if k.is_a?(Symbol)
+              k.to_s.gsub(/__/,".").to_sym
+            else
+              k.dup.gsub(/__/,".")
+            end
+          else
+            k
+          end
+        end
+
+        content.transform_values! do |v|
+          if (v.is_a?(Hash) || v.is_a?(String)) && v.empty?
+            nil
+          else
+            v
+          end
+        end
+      else
         warn "Failed to load #{filename} because it doesn't contain valid YAML hash"
         return {}
       end