When you use fs -getmerge with HDFS, you are guaranteed file list sorting (part-00000, part-00001, onwards). When you use the same with other FSes we bundle, the ordering of listing is not guaranteed at all. This is cause of http://download.oracle.com/javase/6/docs/api/java/io/File.html#list() which we use internally for native file listing.
This should either be documented as a known issue on -getmerge help pages/mans, or a consistent ordering (similar to HDFS) must be applied atop the listing. I suspect the latter only makes it worthy for what we include - while other FSes out there still have to deal with this issue. Perhaps we need a recommendation doc note added to our API?