It seems like java fails to correctly encode Strings when ProcessBuilder or Runtime.exec pass them along to the process they spawn, even with -Dfile.encoding set - for reasons that I don't understand. This means high codepoint characters (Chinese, Japanese etc) don't passed along to the child process.
As a simple example, compile the following two test classes, substituting in your own jre in Test1 and whatever file path you like in Test2:
import java.io.IOException;
import java.nio.charset.Charset;
public class Test1 {
    public static void main(String[] args) throws IOException {
        String s = "因";
        System.out.println(bytesToHex(s.getBytes(Charset.forName("UTF-8"))));
        Runtime.getRuntime().exec(new String[]{"C:\\Program Files\\Java\\jdk1.6.0_45\\bin\\java.exe", "-cp", ".", "Test2", s});
    }
    public static String bytesToHex(byte[] bytes) {
        char[] hexArray = "0123456789ABCDEF".toCharArray();
        char[] hexChars = new char[bytes.length * 2];
        for ( int j = 0; j < bytes.length; j++ ) {
            int v = bytes[j] & 0xFF;
            hexChars[j * 2] = hexArray[v >>> 4];
            hexChars[j * 2 + 1] = hexArray[v & 0x0F];
        }
        return new String(hexChars);
    }
}
and
import java.io.FileWriter;
import java.io.IOException;
import java.nio.charset.Charset;
public class Test2 {
    public static void main(String[] args) throws IOException {
        FileWriter w = null;
        try {
            w = new FileWriter("<some directory>\\testoutput.txt");
            w.write(Test1.bytesToHex(args[0].getBytes(Charset.forName("UTF-8"))));
        } finally {
            if (w != null) w.close();
        }
    }
}
Then run Test1:
java -Dfile.encoding=UTF-8 Test1
Observe that Test1 prints out "E59BA0", whilst Test2 writes "3F" ('?') to file.
Can anyone explain why this is, and what the correct way to accomplish what I want to accomplish is?