When I did echo ^[[21t; > STDOUT.txt 2> STDERR.txt I get nothing in either file, yet I can see the window title on the screen. Putty is returning it, but I can't seem to capture it.

It seems you did not read or at least did not understand my posting.

PuTTY and any other terminal emulator returns answers to status queries on the same channel where it returns user input: STDIN. STandarD INput, not STDOUT, not STDERR. You see the answer on screen because the terminal handling code of your operating system works in echo mode and writes back everything coming in from the terminal back to the terminal. This happens in the kernel, in a layer below the file handle layer.

Stupid example that lacks disabling echo and a reasonable reading routine:

#!/usr/bin/perl -w
use strict;

$|=1;
print
        "Press <Enter> now, as this is a very stupid demo!\n",
        "Note that echo is not turned off, so you will see the answer 
+here,\n",
        "even before perl has read it: ",
        "\x05"; # Ctrl-E -> tell Putty to identify itself
my $id=<STDIN>;
chomp $id;
print "OK, your terminal answered '$id' to Ctrl-E.\n";
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Alexander