I have a "vanilla" site with only some of your plugins. I have activated:
Select Language At Signup,
Set Password on Multisite Blog Creation,
Remove Email Verification,
and Signup TOS.
When a new user sings up I receive an email with an empty Activation Key like:
The user "david" has submitted a manual payment request via the Pro Sites checkout form.
Level: 2 - Next
Period: Every 12 Months
User Email: david@ david.com
Activation Link: http://domain.com/wp-activate.php?key=
Site Address: http://domain.com
Manage Site: http://domain.com/david/wp-admin/
Payment Amount: 100