Hi, after all this time, I picked up the server again to check the problem and for total happiness I managed to solve it!
Remember, I'm using Ubuntu Server 16.04.
I can not tell if it was by default from the beginning, but the 'VirtualHost' in the files "/etc/apache2/sites-available/000-default.conf" and "/etc/apache2/apache2.conf", was as below:
<Directory "/var/www/html">
Options Indexes FollowSymLinks MultiViews
AllowOverride FileInfo
Require all granted
</Directory>
What I did was simply remove 'Indexes' and 'MultiViews', leaving only 'FollowSymLinks', as bellow:
<Directory "/var/www/html">
Options FollowSymLinks
AllowOverride FileInfo
Require all granted
</Directory>
After that, I restarted the apache service and rewrite worked perfectly, causing my problem to be resolved as well, since it was being generated due to this incompatible Apache configuration with whmcs.
Below I put the link that inspired me to make this change:
I leave here my criticism of WHMCS support, as they have a deeper knowledge of Apache and the requirements of their system, could help us in this and save us great waste of time and great loads of stress.
Anyway, thank you for all the help you have received.
Thank you!
Best Regards