open FILE1,"out.prod" or die "Cannot open file $!";

@rec=<FILE1>;
%save=();
foreach $x (@rec) {
  if ( $x =~ /2005/ ) {
    chomp($first=$x);
    $save{$first}=undef;
  }
  if ( $x =~ /time/ ) {
    chomp($lat= $x);
    $lat =~ s/.*?time=(\d+)\.\sms$/$1/;
    if( $lat > "10" ) {
      $save{$first}=$lat; 
      #print "Hash value is $save{$first}\n";
    }
  }
}
foreach $first (sort keys %save) {
  if ($save{$first}) {
    print "hash value is  $save{$first} ms.\n";
  }
}
[download]

If $x !~ /2005/ you have no $first.... thus $first is undef, meaning during the loop it prints out fine, but inside the hash, you're overwriting the same key everytime.

Also, why not just chomp $x at the start and get it over with there instead of chomping twice?