As the title states, on a clean 4.6 installation running as a MySQLi DB Cluster w/ Service Portal installed, the Database Integrity check fails with the following message:

The database is not consistent with the distribution database.

To synchronize your database with the distribution setup, run the following SQL commands:

DROP TABLE ezdbfile;
DROP TABLE ezdbfile_data;

Steps to reproduce

1. Setup MySQLi DB Cluster installation
2. Run the Database integrity check from the Upgrade Check section (in Setup)