#!perl 
use strict; # ALWAYS! (Why? Helps catch typos before run time... among other things)
$|=1; # This disables buffering. JCWren's Suggestion.
my $program = 'c:\progdir\bin\proggie.exe'; 
my $dstfile = 'd:\scripts\log\archive\proggie.log'; 
my $arg0 = '"Blah.Blech.>"'; 
my $timeout = 60; 
open( PRG, "$program $arg0 |") or die "Couldn't open '$program $arg0', $!";
open(LF, ">$finaldest") or die $!; 
my $inloop = 0;
my $endtime = time + $timeout; # Only do the math once.
while( <PRG> and $endtime >= time  ) # '>=' or '>', your choice.
{ 
  if( not $inloop )
  {
    # This will get run the first time, but not after.
    # As per JCWren's Suggestion.
    print STDERR "Inside Loop\n";
    $inloop = 1;
  }
  chomp;
  print LF $_, "\n"; 
} 
close(LF) or die $!; 
close(PRG) or die $!;