You've opened your file for reading and writing, which is good, but after you read in the file, you don't seek back to the beginning. So, you're appending the modified lines at the end of the existing contents.

The easiest way to modify a file in place is probably to use Perl's nifty in-place editing feature. Here's one way of doing it:

#!/usr/bin/perl -i.bak
# in-place editing; save the original file with a .bak extension

use Win32::Console;
use strict;


open(STDERR, ">error.log") or die "Can't open error log: $!\n";

my $con = Win32::Console->new();

$con->Mode(ENABLE_WINDOW_INPUT | ENABLE_PROCESSED_INPUT |
           ENABLE_LINE_INPUT | ENABLE_ECHO_INPUT |
           ENABLE_PROCESSED_OUTPUT | ENABLE_WRAP_AT_EOL_OUTPUT);

$con->Display;

$con->Write("Please enter the agent ID number: ");

chomp(my $port = <STDIN>);

$con->Write("The port number to use is $port.\n"); #Debug stuff, this 
+works

{
  local @ARGV = "c:\\blah.txt";
  # set up a temporary @ARGV for in-place editing

  while (<>) {
    s/serverport 111$/serverport $port/;
    print;
  }
}
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All you have to do is use the -i switch and put the name of the file(s) to change in @ARGV. Then you can just read in lines with <>, modify them, and print them back out.

See perlrun for more about Perl's -i command line switch.