Looks fine to me....

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

my $number='1234567890.01'; # with commas, should be "1,234,567,890.01
+" 
print "N=$number\n";

$number =~ s/(\d)(?=(\d{3})+(\D|$))/$1\,/g;
print "N=$number\n";
[download]

Output

N=1234567890.01
N=1,234,567,890.01
[download]

Care to elaborate on which part doesn't work?

-Blake