Ah, I see, the code in Configuration has been changed in hadoop-2. The Configuration object only adds core-default.xml and core-site.xml, but things like mapred-default.xml and mapred-site.xml get added in a static{} block of mapred.JobConf.

If you are loading mapred-site.xml you should also load mapred-default.xml. If these are not already default resources, maybe the right thing to do is classload JobConf?