Permissions Issues on network – users disappearing, plug-in discrepancy?

I am trying to use a bundle of plugins from WPMUdev.

Kimberly has helped me get Pro Sites partially up and running – however, in the last week, since installing Easy Blogging and New Blog Templates to work in conjunction with Pro Sites, I must have missed a setting or three along the way.

Logged in as Super Admin, on the Network Admin user list, I can see all of the users and the sites that are subscribed to. However, logging in to my main site (http://loveandlightnetwork.org) to look at the users solely on it, several of the names disappear, even though they are on the Network Admin list – and indicated as being part of that site.

If one of those users tries to log in to the main site, they can get in, but they have no permissions any longer. They don’t have access to the dashboard or to post new blogs. Several of these users should be Authors, but have no permissions and receive the error stating so when they try to access the dashboard.

As the Super Admin, when I try to ‘add’ the user to the specific site, I am told the user already exists on that site.

In a search for these users, they don’t show up. They don’t show up in the list, either.

I’m starting to get frustrated.

I disabled the Pro Sites this morning, and the ability for users to create a new site. I’m hoping to very soon get all the bugs worked out so that my time is spent promoting and maintaining the site instead of trouble-shooting while building. It’s definitely not my forte.

Thanks!