You need to diversify your strings
Not much to comment on the permutation, but generally speaking you should use try-with-resources, Files.lines() and a healthy dose of Java 8 features for your main() method:

public static void main(String[] args) throws FileNotFoundException {
    try(Stream&lt;String&gt; lines = Files.lines(Paths.get(args[0]))) {
        lines.map(PermutateString::sortString)
                .map(PermutateString::permutateString)
                .forEach(System.out::println);
    } catch (IOException e) {
        // do something with this, e.g. show file not found message?
    }
}


Please check the use of Paths.get() for your case too...