Thats interesting the email phrase has this
In register.php when sending the email we replace certain variables.
Content visible to verified customers only.
Not ^theuid is being replaced with $theuid so I am not seeing why your userid should be empty there. No one else has reported this issue and the coding in this file has been the same way since version 3.1 so for a year.
I will see about setting up a test site and verify everything works and if so we might need to see your files.