Description of my issue:
When the setting to encrypt the configuration in the global Akeebabackup settings is on then the command line (cli) akeeba-backup.php script gets an empty ini_data_local variable in the AEPlatformAbstract->load_configuration function after decryption.
This causes the script to run with the default settings and not the profile settings.
When this security setting is off then the ini_data_local variable holds the profile settings string to parse and the right profile settings are used.
I debugged this by just echoing and catching the output in the cronjob email.