A customer had installed SCCM 2012 and uses it for EndPoint Protection only for now. Half of the clients did not get the updateded definitions. I had a look on the deployment, and it gave this error: 0X87D00692 Group policy conflict.
Did a check on group polices that applied to the workstations, and one of them had configured a former WSUS server as Update point. Removed that, and not long after the clients started getting their new definitions