Login and Register is missing and not working properly

Hi there,

I'm having a weird issue with my multisite. Users can't login properly. At first I thought it had something to do with my Theme (missing buttons: login and register) Then I found out that when users want to login via the default ACCOUNT page (from Membership Pro 2) they would redirect to the home page without being logged in.

I tried to:
Deactivate all plugins.
Used original theme instead of child theme.
Compared options and setting with my other multisites (similar setup)
Deleted Cache
Rebooted my WHM

So far no success.
I was working properly yesterday as far as I know. Changes I did to my VPS was a while back. Moving to PHP7 and changed over from subdomain to subfolder structure. Same thing with my other 2 VPS setups... No problem there.

Just this one that is causing me headaches.
Anyone have some clues on this one?

Link where to problem is: http://cu2.co.nz
And see here how it supposed to look like with the login/ register buttons on the top: http://careertiger.co.nz

PS
I already activated SUPPORT ACCESS in case anyone from support staff wants to have a peek.

Cheers,
Ronald