User Signup - Email Contains Wrong Domain

I have a strange issue on a Multisite. When I sign up as a user on the main site (mainsite.com), the link in the confirmation email is for a subdomain (subdomain.mainsite.com). Ironically, when I click it, I am directed to the subdomain site and confirmed. The username/password are provided as if I had originally intended to sign up on the subdomain.

Where is this being controlled? I have wpmu-assist in MU plugins. Could this be causing problems? I will remove this and test again.

What else could cause this? Where else might I look to trouble shoot this?

Thanks,
Chris