Heya Chrimera,
This shouldn't happen, have done 3 upgrades on different boards and haven't had this problem before. Before im able to help, i need some more info.
Is an error produced? and if so, what is the error?
Also, can you tell me how you have permissions set on the private forum which users are gaining access to? is Restrict Viewing and Writing of Posts To Administrators, the forum Moderator, and other authorized* users checked? And is a password set?
Are registered users gaining access? How about unregistered users?
I'll help find the problem. Just give me some more info -- i'll be around all night.
Also, your domain keeps bouncing back my emails with SMTP errors. Do you have another email address? If so, PM me!