The after registration message is not sent through substitutions so you can't use substitutions there. What email are you putting those substitutions in? They should work fine in the registration emails in CB > Configuration > Registration.
This has always worked before today.
Then revert whatever change you made. As whatever you changed appears to have broken it. Substitutions failing suggests no user object is present. Try changing your registration emails back to the following defaults and see if they work.
CB > Configuration > Registration
Pending Email Body: YOUR_REGISTRATION_IS_PENDING_APPROVAL_MESSAGE
Welcome Email Body: YOUR_REGISTRATION_IS_APPROVED_MESSAGE