Hi.
I've had the same issue, on my test server (in the beginning sep 11, then upgraded to 12.1 and now upgraded to 12.1RU1).
On the error message popup I clicked on "cancel".
I re-run the installation process and I choose "Repair". After that, the Management Server Configuration Wizard started as if this was my first installation or a Disaster Recovery operation.
I checked the information about site name, ports, DB type and, after typing the DB's password (for the user SEM5) the process told me my DB had not been upgraded to the latest schema, so the DB Upgrade Wizard started.
After the operation completed, the SEP manager service started and I logged correctly into the console.
I'll open a ticket to the support to have more info about this issue, because in the next months I will upgrade lots of SEP managers of our customers.