I recently purchased Membership to install on my site but

I recently purchased Membership to install on my site but it created issues. The installation was fine but the plugin ended up re-writing my permissions, which led to losing all of my navigation within my dashboard (pages, posts, etc). GoDaddy is my host and they told me this. They were able to repair, deactivate the plugin so I could get back into the site but suggested contacting you prior to reactivating it in case this happens again. I really need to use this plugin to set up a membership site but don't want to run into this issue again. Any help or insight would be much appreciated.