diff --git a/lib/puppet/util/settings.rb b/lib/puppet/util/settings.rb
index a91b0d6..576aeaf 100644
--- a/lib/puppet/util/settings.rb
+++ b/lib/puppet/util/settings.rb
@@ -78,7 +78,7 @@ class Puppet::Util::Settings
             config = trans.to_catalog
             config.store_state = false
             config.apply
-            config.clear
+            config.clear(true)
         rescue => detail
             if Puppet[:trace]
                 puts detail.backtrace
@@ -683,7 +683,7 @@ Generated on #{Time.now}.
                     raise "Could not configure for running; got %s failure(s)" % failures
                 end
             end
-            config.clear
+            config.clear(true)

             sections.each { |s| @used << s }
             @used.uniq