I'm using the default users module, but I've found something now that Chestnut has told me to register a user myself.
I have omitted some info that might be interesting, sorry for that. My two websites are mysyte.com and subdomain.mysyte.com and the subdomain one is sharing some
DB tables with the original one, in this case all the ones referred to users. And now, registering a user myself I've found that when I register a user in mysyte.com it doesn't enter any group at subdomain.mysyte.com and viceversa, but it works correctly in the site where I register it.
Does that help you in any way?