It doesn't matter much.
just take care that you don't have two domains with the same content.
www.example.com and example.com are different sites to Google and have different cookies as well.
www.example.com and example.com are different sites to Google and have different cookies as well.
http://www.google.com/webmasters/
Although, the preferred way is probably to use a redirect.
it looks like they did fix the problem though: site.com 301's to www and they now set cookies on .site.com