My membership plugin is protecting all pages on the site when I don't want it to.

My membership plugin has been running really well, but now it is acting very strange. I have set different access levels for users with some seeing all pages and some seeing limited amounts of my website. Now, it is protecting all of my content, even when I have set the permissions to show everything. We had to install a "maintenance mode" plugin to hide the whole site from view recently and though we have deactivated it and uninstalled it, I am wondering if this is causing problems? We were able to get the membership running correctly for a few hours today, but then out of nowhere it set all content to protection mode and I haven't been able to fix it since.

Thanks for the help in advance!
Court