The only way we were able to fix that problem was to reinstall SEPM on the servers were we got the error message.But don't worry.... it's actually quite easy to reinstall SEPM on a server:
1. Stop the SEPM-services on the server, where you want to reinstall SEPM.
2. Log into a another SEPM in the same site and delete the SEPM that you want to reinstall.
3. Uninstall SEPM on the server, where you want to reinstall SEPM.
4. After SEPM is uninstalled, then reboot the server.
5. Install SEPM again, and add it to an existing site.
And the problem is fixed :-)