Super Admin can’t see all Menu’s

Hi,

Since a while I notice a issue on my Multisite WordPress Network (4.7.3): The Superadmin can’t see all menu’s that supposed to be in the Network Dashboard.

I use BackupWordpress for simple backups/exports of my installation, that plugin should get it’s own menu under Settings > Network Settings. Strangely, I don’t see that menu.
I do notice the plugin is doing it’s job automatically because when I navigate to the BackupWordpress folder via SFTP I see daily backups.
When I navigate to the BackupWordpress url manually I get the ‘You do not have sufficient permissions to access this page’ error.

Further details on my installation:
Network Activated Plugins:
– W3TC
– iThemes Security
– Really Simple SSL
– Google Authenticator
– Yoast SEO
– WP Change Default Email
– BackupWordpress (ofcourse…)
Wordpress version: 4.7.3
I already tried turning plugins on and off again, doesn’t do anything.
I have about 5 domain mapped subsites and about 10 subsites on a subdomain.

What could be going wrong here?

Thanks a lot,
Jo?l van Daalen