Might the file that is being uploaded by an image or an mp3 or some other binary file? If so your reading routing ought to look something more like this:

    my $filehandle = $q->param('file');
     my($buffer,$bytesread,$has_data);
    if( $cfg{filetype} eq 'binary' ) {
        open(OUTFILE,">$cfg{savename}") 
            or return("Couldn't open '$cfg{savename}' for writing: $!"
+);
        binmode OUTFILE;
        while ( $bytesread=read($original_name,$buffer,$cfg{max_bytes}
+)) {
            print OUTFILE $buffer;
            $has_data++;
        }
        close OUTFILE
        or return("Couldn't close '$cfg{savename}': $!");
        if(!defined $bytesread) { return("$!"); }
    } 
    else {
        open(OUTFILE,">$cfg{savename}")
            or return("Couldn't open '$cfg{savename}' for writing: $!"
+);
        while (<$original_name>) {
            print OUTFILE;
            $has_data++;
        }
        close OUTFILE
        or return("Couldn't close '$cfg{savename}': $!");
    }
    if( !$has_data ) { 
        return(qq/
            Nothing in '$original_name'.<br>
            It either doesn't exist, or is empty.'
        /); 
    }
    return '';
[download]

You should also have something like this unless you like DOS attacks:

$CGI::POST_MAX = $cfg{max_bytes};