The activation button in the confirmation email didn't have the site url in it for some reason. Tracing the code, I noticed that the siteurproperty is blank when the message is sent. I do have a value for siteurl. The issue seems to be an issue with the emailtempate sitesettings property not being initialized at the correct time.
I am not sure if I am the only one getting these issues. I am doing quick fixes in the code and I know they are not suitable for pull requests. I am trying to get the wiki working 100% at quickly as possible.