FSUtils.getRootDir() just takes a configuration object, which is used to:
1) Get the name of the root directory
2) Create a filesystem (based on the configured scheme)
3) Qualify the root onto the filesystem
However, the FileSystem from the master filesystem won't generate the correctly qualified root directory under hadoop-2.0 (though it works fine on hadoop-1.0). Seems to be an issue with the configuration parameters.