Please explain cause of message "App [msqlr6] invalid configuration found"

You're getting the message because you altered the MySQL databases. Whenever installing an app provided through Netgear or any of their partners, the app relies on default directory configurations and will produce this error if you have made any changes to the MySQL settings. You have two options for completing the installation as you described; 

1. Restore the default settings before installing the application and change the directories manually after a successful installation.
2. Perform a custom installation using the files directly from the app developer and skip the ReadyNAS interface altogether (I did this when I installed Moodle 3.0).

P.S. The error is probably occurring because you switched to an SSL connection requiring the use of a port that is most likely not in the default settings. It sounds like you have already successfully installed the application, so if this just a matter of setting up SSL, you need to follow along the lines of recommendation #2. You may not need to get the files straight from the developer, but you will need to know enough about the configuration files to edit the connection ports. 

Good Luck!