I'm having the same problem, being the platform admin for a large site I received numerous replies from students already on the platform admin e-mail. Strange thing is that I do have a no-reply address set.
There doesn't seem to be a setting to change this to the coursemanager's e-mail, so I guess this is a bug in 1.9?
jmontoya, do you mean that if this setting has a value, e-mails are sent from the coursemanager's address? I have a no-reply address set, but all e-mails from any course are sent with the platform admin's name and e-mail.