Hi Juan,
I tried the following process and it worked correctly:
- Created 2 sites in an installation
- Deleted the global "Membership - Registration" email template
- Created a "Membership - registration" email for each site (using the site selector in the Email Templates UI)
- Registered user on Site 1
- Received Site 1 email template
- Registered user on Site 2
- Received Site 2 email template
If you go through these steps, do you get the same results? Any info you can provide will help!