#!/usr/bin/perl

use strict;

my $inFile = "TST5.NDM.SB.IOWSFLAT.STMTS.MRDF.TEST";
my $outFile = "$inFile.out";
my $buff;

open(INFP, $inFile);
open(OUTFP, ">$outFile");
binmode(INFP);
binmode(OUTFP); 

my $cnt = 1;
my $matchCnt = 0;

while (read(INFP, $buff, 128)) {

  print OUTFP $buff;
  
  my $target = "\x0D";
  if ($buff =~ /$target/) {
    print $buff;
    print "\n found \$target on 'line' $cnt, ";
    print "'" . ord($&) . "', '\x$&'\n";
    ++$matchCnt;
  }
  ++$cnt;
}

print "found target $matchCnt times\n";
close (INFP);
close (OUTFP);

Either you looked at the file using UltraEdit or you're running on AIX. Both aren't possible since UltraEdit doesn't run on AIX.

Did you perhaps FTP the file between the two systems using ASC mode?