I'll elaborate a bit on his one more bug. Let's walk through your program ;)

use strict;
use warnings;
use win32::ole;
[download]

You should get used to write module names in the right case (here: Win32::OLE), or your programs will throw "module foo::bar not found in @INC..." errors if they are ever run on a case-sensitive file system.

my ($f_mfg_desk, $f_mfg_desk_output, $record,@wip_query, $wip_query, $
+opr_cd, @header,
    $header, %header, $x, $row, $row_array, @row_array, @rule_array, $
+BREAK,
    $year, $month, $day, $hour, $min, $sec, $run_time, $dtme,
    $local_outfile_timestamp, $remote_outfile_timestamp, $local_outfil
+e_latest,
    $remote_outfile_web, $Oper_Cd, $Pick_Ref_Num, $Part_Id, @header_da
+ta,
    $newrow, @newrow, $head);
[download]

ugh.
There's nothing wrong with globals if there are just a few and their use is justified. Blindly declaring all variables as globals begs for trouble. You should read about scoping.

# This gets the document from the server
$f_mfg_desk = '//142.22.50.34/planning/logistics/programs/wip_query.tx
+t';
[download]

This assigns a scalar and does not "get" anything. (cut & paste reduce problem fragment?)

...

open (INFILE, '//163.10.50.33/planning/logistics/programs/chicago_wip_
+query.txt');
while (<INFILE>) {
    $record = $_;
    chomp($record);
    @newrow = split(/\t/,$record);
[download]

A good example of bad scoping. $record here is just used within the loop, so you'd better write that as

while (my $record = <INFILE>) {
[download]

Also, you are just using $record to chomp and split it, so after all your code would be smarter written

while (<INFILE>) {
    chomp;
    @newrow = split /\t/;
[download]

which is a bit shorter and more concise.

    $header_data{$newrow[2]} = [$newrow[3], $newrow[4], $newrow[5], $n
+ewrow[6], $newrow[7], $newrow[8], $newrow[9], $newrow[10], $newrow[11
+], $newrow[12], $newrow[13], $newrow[14], $newrow[15], $newrow[16], $
+newrow[17], $newrow[18]];
    }
[download]

This also can be written with a bit less effort.

$header_data{$newrow[2]} = [@newrow[3..18]];
[download]

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