I was able to fix this issue on my setup. I am not sure why this would have changed but I noticed that my Apache server conf file for Matomo had the wrong directory defined for options. This needed to be be updated and then the AllowOverride All option would be applied to the Matomo directories.
Current working config files:
Matomo.conf - Old
<Directory /var/www/html/matomo/>
Options FollowSymlinks
AllowOverride All
Require all granted
</Directory>
Matomo.conf - New
<Directory /datadrive/www/html/matomo/>
Options FollowSymlinks
AllowOverride All
Require all granted
</Directory>
This has resolved the issue in my setup.
My configuration:
Server version:Ubuntu 18.04.5
Apache Version: Apache/2.4.29
Mysql: Ver 15.1 Distrib 10.1.48-MariaDB
PHP Version: 7.2
Matamo Version: 4.3.1