I have been struggling with this as well. What I have observed through trial and error (don't take this to be an authoritative answer):

• The Website Name must match the domain name. The field Website Domain field is apparently not used. (Or at least not consistently)

• Versioning and A/B testing must be enabled

• After creating a second site, it seems they are initially still referring to the the same master version. When I create and activate a new version for each website, then I get different content in each website.

• There also seem to be some caching issues when saving a version and then logging out in the same session. So it's best to always open a separate session to observe the result.
  

yes, the domains all point to the same instance, however regardless of the domain you use they all seem use the same website and company.

not sure why this is happening.

Have you pointed those 3 domains to your Odoo instance?

BTW, please give ERPOnline a try. It supports Odoo 9 with multiple websites very well.