I tested this on my WinXP 32 bit machine. It works fine. Something is wrong with your command line, what I don't know. But there is no fundamental need to escape the " characters. A side effect of a Windoze command line could be true.

#!/usr/bin/perl
use warnings;
use strict;

my %accounts = (
  tom =>  "BigApple",
  tom2 => "BigApple2",
  tom3 => "BigApple3",
  tom4 => "BigApple4",
  tom5 => "BigApple5",
  tom6 => "BigApple6",
  tom7 => "BigApple7",
);
# sort the users in descending order
my $counter = 1;
for my $userID (reverse sort keys %accounts) {
  print "$userID\t";
  print "\n" if $counter++ % 3 == 0;
}

__END__
Prints:

tom7    tom6    tom5    
tom4    tom3    tom2    
tom
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