I started writing an answer to your question when I realised there were other possibilities. Therefore, I retract my claim.

I'll have another look when you post the code that suffers from the problem you are describing. (There is only one response in the code you posted.)

Here is my code in it's entirety.

#!/usr/bin/perl -w

BEGIN{
    $ENV{SYBASE} = "/opt/sybase";
}
BEGIN{

        $ENV{LD_LIBRARY_PATH} = "/usr/local/samba/lib";
        print "env is $ENV{LD_LIBRARY_PATH}\n" if $DEBUG;
}
BEGIN{

        $ENV{LIBPATH} = "/usr/local/samba/lib";
        print "env is $ENV{LIBPATH}\n" if $DEBUG;
}

#Modules
use IO::Socket::INET;
use Sybase::CTlib;
use Date::Calc ":all";
use Carp;
use Crypt::CBC; 
      
#Declare Variables
my $DEBUG=0; #Set to one for comments
my $OrderId;
my $HashOrderId;
my $msg;
my $key = "integration";
my $iv = pack("H16", "0123456789ABCDEF");
my $web_address = "http://webpinspdfdev/powerchartaccess/ViewPDF?o="; 
+#Will need to be changed for production
my $ciphertext;
my $cipher;
my $DIR;
my $idxcount = 0;
my $out_file = "/opt/impact55/Hash_PDF/out_file_$idxcount.dat";

#Source Code

$BASEPATH = "/opt/impact55/Hash_PDF";
$APP = $ARGV[0];

problem ("You must supply one APP as an argument!") 
unless ($#ARGV == 0);

if($APP eq "PFT"){$DIR = "PFT"} #Set file directory

my @transactions = glob("$BASEPATH/$DIR/PDF_${APP}_*.tmp"); #put all f
+iles in array
print "transactions: @transactions\n" if $DEBUG;

if($APP eq "PFT"){

    #for each file in array
    foreach my $in_file (@transactions){

        print "in_file: $in_file\n" if $DEBUG;

        open(FH,$in_file);
        @lines = <FH>;
        close(FH);
        
        $idxcount++;
        
        #set encryption
        $cipher = Crypt::CBC->new( -key    => $key,
                           -cipher => 'Crypt::Blowfish',
                           -header => 'none',
                           -iv => $iv);
                                                   

            #Cycle through transaction
            foreach my $line (@lines) {
        
                #Pull individual segments
                my($MSH,$PID,$ORC,$OBR,$OrderId) =
               $line =~ m{(MSH\|.*)\r #MSH segment
                               (PID\|.*)\r #PID Segment
                               (ORC\|.*)\r #ORC Segment
                               (OBR\|.*)\r #OBR Segment
                               OrderId\:(\w+\_\d+)\r}smx; #Order Id to
+ be hashed
                               $OrderId = $OrderId;
                               
                               print "MSH: $MSH\n" if $DEBUG;
                               print "PID: $PID\n" if $DEBUG;
                               print "ORC: $ORC\n" if $DEBUG;
                             print "OBR: $OBR\n" if $DEBUG;
           
                    #Encypt Order Id
                    $ciphertext = $cipher->encrypt_hex($OrderId); 
                    print "Crypted Order Id: $ciphertext\n" if $DEBUG;
                
                    #Build OBX segment
                    my $OBX = "OBX|1|RP|100.214||";
                    $OBX .= $web_address;
                    $OBX .= $ciphertext;
                    $OBX .= "||||||||||";
                    print "OBX: $OBX\n" if $DEBUG;
                    
                    #Build Message
                    $msg = sprintf "\013";
                    $msg .= sprintf "$MSH\015";
                    $msg .= sprintf "$PID\r";
                    $msg .= sprintf "$ORC\015";
                    $msg .= sprintf "$OBR\015";
                    $msg .= sprintf "$OBX\034\015";
                    print "MSG: $msg\n" if $DEBUG;
                    
                    #Output
                    if($DEBUG){
                    open(my $FHOUT,">$out_file");
                    print $FHOUT $msg;
                    close($FHOUT);
                    }
                    else{
                        #Create the connection
                        my $socket = IO::Socket::INET->new( 
                                Proto => 'tcp',
                                PeerHost => 'axtcnr:6540',
                                ) or die("Can't connect to axtcnr:6540
+: $!\n");
                                
                            
                        #Send transaction
                      if($msg =~ m{(\013.*\034\015)}smx){
                          print $socket $1;
                      }
                      
                      #Shutdown sending only receive
                      $socket->shutdown(1);
                      
                      #Read response
                      $socket->recv($rv,1024);
                        print "Received from Server : $rv\n";
                        


                    }
                    
            
        
            }
    }
}
[download]

You create a new connection for each file. If $1 contains the correct string, that means the server is sending the response that's meant for one connection to an entirely unrelated connection. A server bug.

PS — $sock is a socket, so you can use it with <> (e.g. local $/; <$sock>) just like you did before you switched to IO::Socket::INET.