I've changed your code to read:

if (fork()==0) {
   print "child1\n";
   system ("ls -al $ARGV[0]");
   exit;
}
if (fork()==0) {
   print "child2\n";
   system ("df -k $ARGV[1]");
   exit;
}
wait;
wait;
print "Done!\n";
[download]

and it works fine. So your problem might be one or both of:

1. The programs you call don't work as you think they should.
2. You can't seperate the ouput by looking at it. The lines of output usually are mixed.