I've seen this issue on a couple of occasions with both EMM 11.0 and 12.0. The issue is cause by a conflict with existing database entries. The resolution was to start by creating a backup of ePO as detailed in knowledgebase article KB66616. Open the ePO database in Microsoft Studio Manager and go to the table Orion.DashboardPage and delete any rows with EMM in the name. Retry the check-in of the EMM extension and you should find it works.
If you get any issues with the process you can roll back by following the restore process as per KB66616, but make sure you have the ePO installation files for the version you're running together with the backup prior to amending any database entries.
Many thanks for this, it worked perfectly and saved me the whole MER reporting process to boot!