Thank you markkawika, so simple it was brilliant. When you do this on console it still prompts for Destination filename. So I didn't think it would work. But using the below in the script works everytime:

  my $copy = ("copy tftp://10.148.48.52/cat4500-ipbasek9-mz.122-31.SGA
+9.bin bootflash:cat4500-ipbasek9-mz.122-31.SGA9.bin");
    $session_obj->input_log(*STDOUT);
    $session_obj->begin_privileged($userinfo[1]);
    $session_obj->cmd("$copy");
    $session_obj->cmd("cat4500-ipbasek9-mz.122-31.SGA9.bin");
    $session_obj->close;
[download]

Thank you