I'm having the same problem with an added twist.
On the site I'm working with, we have two membership systems---regular and special. Special memebrs are in Joomla's 'author' class and regular members are in the 'registered' class. Special memembers have to pay for their subscrition.

We're using MamboCharge from JoomlaWare to enable registrations into the special class.

Anyone who was registered this way can access the 'registered' and 'special' sections of the site.

However, there are a few people who I've added to the author class manually. Since I installed Joomla-SMF RC1, these people haven't been able to gain access to the restricted sections.

People I manually add into the backend have access though.

I was almost certain the problem might be something in JoomlaWare's software but now that I uninstalled JoomlaSMF, everything works correctly.

Kum, I am assuming the additional membership system is looking for something in the cookie that is unique to it.  Probably similar to JACL which patches joomla.php and adds code to the login sequence.  Do you know if it is patching any core joomla files?

I found a solution to my problem. I created a subscription that charged $0 per year and lasted initially for 10 years then I put everyone that I had manualled added into the author class into that subscription. Voilla! It worked.

I didn't think it was patching any of the core files since its installed as a component and doesnt' request to patch any pre existing files.

Now I'm not so certain. I think the only way it could control who gets to access which pages like that is if it had made some change to the core files.