This is a really frustrating one.

I have setup a nginx fastCGI server (debian), with a multisite install. All kind of works, however:

Essentially wordpress URL paths are incorrect for links that are on the front-end of a website, they just redirect to the current page, it does not add the url extension required (i.e. "my account" link for a woocommerce link or similar) and on the backend theme/plugin activation links are wrong. There are bits missing out of the URL path.

For example, where the URL should be:
example.com/wp-admin/network/themes.php?page=install-required-plugins

I get:
example.com/wp-admin/themes.php?page=install-required-plugins

Which is incorrect and results with a permission issue.

Another example, what should be:
example.com/wp-admin/network/admin.php?page=WordfenceSecOpt (selectable from side menu)
has a link from the dashboard of:
example.com/wp-admin/admin.php?page=WordfenceSecOpt

As you can see it is stripping the full URL path.

I thought this may be plugins themes etc. so I disabled everything and tried, then removed everything and tried, no avail.

Then thinking it is likely FastCGI, Nginx or similar, I went about setting up a completely separate server, with a different LEMP configuration and nothing on it. Once again, the same has occurred.

Having tried too many times to count, crashing both servers several time and 2 days of Google'ing I have given up.

I'm hoping someone here could help point me in the right direction?