File.listFiles() mangles unicode names with JDK 6 (Unicode Normalization issues)

I'm struggling with a strange file name encoding issue when listing directory contents in Java 6 on both OS X and Linux: the File.listFiles() and related methods seem to return file names in a different encoding than the rest of the system.

Note that it is not merely the display of these file names that is causing me problems. I'm mainly interested in doing a comparison of file names with a remote file storage system, so I care more about the content of the name strings than the character encoding used to print output.

Here is a program to demonstrate. It creates a file with a Unicode name then prints out URL-encoded versions of the file names obtained from the directly-created File, and the same file when listed under a parent directory (you should run this code in an empty directory). The results show the different encoding returned by the File.listFiles() method.

String fileName = "Trîcky Nåme";
File file = new File(fileName);
file.createNewFile();
System.out.println("File name: " + URLEncoder.encode(file.getName(), "UTF-8"));

// Get parent (current) dir and list file contents
File parentDir = file.getAbsoluteFile().getParentFile();
File[] children = parentDir.listFiles();
for (File child: children) {
    System.out.println("Listed name: " + URLEncoder.encode(child.getName(), "UTF-8"));
}

Here's what I get when I run this test code on my systems. Note the %CC versus %C3 character representations.

OS X Snow Leopard:

File name: Tri%CC%82cky+Na%CC%8Ame
Listed name: Tr%C3%AEcky+N%C3%A5me

$ java -version
java version "1.6.0_20"
Java(TM) SE Runtime Environment (build 1.6.0_20-b02-279-10M3065)
Java HotSpot(TM) 64-Bit Server VM (build 16.3-b01-279, mixed mode)

KUbuntu Linux (running in a VM on same OS X system):

File name: Tri%CC%82cky+Na%CC%8Ame
Listed name: Tr%C3%AEcky+N%C3%A5me

$ java -ve