Hi,
The registration confirmation email uses the same settings from Web.config/user.config it does not use the system.net.mailsettings, only password recovery uses that.
I would test first using the contact form as discussed here:
http://www.mojoportal.com/emailconfiguration.aspx
For WebStore there are settings for the email from address in the store settings that you need to configure.
Hope it helps,
Joe