I'm still confused. I have a site login/authentication system that does not use cookies and so I want to make it so that miniBB does not use cookies either, but that when the user logins into my system it logs them into miniBB and when users logout of my system it logs them out of miniBB.

Can someone explain how to do this?

As far as I'm aware it just uses application variables for authentication and no form of cookie. I'm not sure if this is the same as sessions?

Either way, I'm also having problems with logging in just using the board login fields. When the user creates a new account on MY system, new accounts also appear for the forums, but when you try to login using the forum login it says the password is incorrect, even though it works for logging into MY system.

My system doesn't encrypt the password using MD5, could that be the problem?

Nobody is able to determine custom problems in your system. We are providing only paid support on that topic.

As about sessions - it is very possible to implement minibb with them, we already did it for some customers... the main idea is that in all functions of bb_cookie.php file, instead of setting/reading login, password from cookies, you need to use $_SESSION variable instead.

Default encryption is defined in function writeUserPwd() of the same file.