Ah yes, that's it.
Related to the fact that I didn't fully understand the code I used from the last question, I've gone bright red :-/
Change the line return if $length <= ++$pos; to the lines

if ($length <= ++$pos){
    close (PERMUTEOUT) ||die "Could not close $permutelist_filename: $
+!";
    return ($permutelist_filename);
            }
[download]

And it all works as expected. My apologies for wasting your time on this one and thanks to all of you for your help.