Oh, I see that the "System email address" can only be changed by a site admin. I have changed it to your email address.
The "Users" group is the default permissions group that is available in all new projects. When we create a new project on PanoramaWeb we add the project administrator to this group, and give this group read access in the project As a project admin you can create new groups, and manage existing ones. Groups make it convenient to grant a particular role / permission to a set of users. You can read more about project groups here: https://www.labkey.org/Documentation/wiki-page.view?name=projectGroups
When a new folder is created in a project it inherits permissions from the project, so all project admins automatically become administrators in the folder. However, the person who created the folder (and anyone else who is a folder administrator) can uncheck "inherit permissions from parent" and adjust the permissions on the folder as they like. That is probably why you cannot access some folders. I don't think there is a way to prevent this but I will check. Also, there might be some folders that were created before you became project admin. If a folder admin had customized the permissions on those folders before you became project admin then you would not automatically be granted folder admin permission.