Theme Customization not working on Multi Site Network Manager website

I have a multisite network. Theme customization works in all of the websites except for the main network manager website. I hope this is clear
When I try to edit and save (even though I don't see anything except for the customizer menu) I sometimes get a message that says (rough translation) "invalid setting".
I tried disabling all plugins, switching themes, giving permissions.

Plugin conflict test doesn't give any results.
Customizer doesn't work on all other themes too.
Already performed troubleshooting:
re-installing wordpress files,
increasing memory limit,
adding define('CONCATENATE_SCRIPTS', false); to wp-config.php
adding remove_action('shutdown', 'wp_ob_end_flush_all', 1); to functions.php
checking permissions to files and directories.

Nothing helps.