I found this post after experiencing the same thing - the confirmation email was going out even if the "Send Confirmation" flag was set to "No". I am using CB1.1 with J!1.15.
I've tried to fix this by changing the call to the activateUser function in components/com_comprofiler/comprofiler.php around line 1300 to:
[code:1] $messagesToUser = activateUser( $user[0], 1, "UserRegistration", $mailToAdmins = $ueConfig, $mailToUser = $ueConfig);[/code:1]
I'm still testing this, but it seems these parameters were missing from the call to the activateUser function which defaults the moderatoEmail and confirmation parameters to "TRUE".