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even when they have no content in them...

This is a system setup issue that is related to the database user permission in use by Flow.

Database User Permissions Required

The user needs to have these permissions assigned:

ALTER
ALTER ROUTINE
CREATE
CREATE ROUTINE
CREATE TEMPORARY TABLES
CREATE VIEW
DELETE
DROP
EVENT
EXECUTE
INDEX
INSERT
LOCK TABLES
REFERENCES
SELECT
SHOW VIEW
TRIGGER
UPDATE

Setting User Permissions

SQLyog 12

Look for the User Manager icon:

Then select the user and choose to set either global privileges or object level privileges (to limit the user to specific databases)

MySQL Workbench 6.2

Look for Users and Privileges in the management tab/section

Then select the user and choose to set either global privileges or object level privileges (to limit the user to specific databases)