It is a manifestation of a bug. Please follow the status of the bug here.
As a workaround please try the following steps:
- Add SSL to the instance (if one is not in place)
- Connect using user = root with the SSL
- Remove the user root@%
- Uncheck (if checked) the "Only allow SSL connections"
- Set the root password again
- Now try and connect with user = root and the password that was set.