I agree with the previous comment, but would like to comment on the problem anyway ...

if (-f "$dir/$file") {
            print "SEND $dir/$file to ftp server\n";
            &Put_File($dir, $file);
        }
        else {
[download]

This test doesn't make sense in the context of what you are doing. If I'm seeing it correctly, this check should always pass, because you got the filename from the readdir just above. I think you possibly meant to check that the file exists on the remote side?

HTH

UPDATE: now I see what's being done. D'oh!