This is supper strange - I just spent like 10 hours trying to workout why my site is not working. Where the heck is the redirection to www stored?
In the end I also noted that the only way to have the site use www. is to create it that way. However I cannot see any difference in the site-avalailbe/domain.com.conf file!
If you setup your site as usual with nginy - you get no database connection - as www.domain.com as server_name seems to whack everything up. I even fully put in a working nginx.conf from my old server - not using any of the filed usually included with "include" - and well got a redirect loop too.
Oh and this should be a high priority item on any guide on migrating your site into easyengine. Right now if your site is www - you'll freak out.