Sander,
it looks like you have not given access to additional AD OU for Intel AMT $iME computer objects to account that is runnig AMT Configurator (for HBC is is executed as SCCM agent - client computer account) or RCS service logon account for Remote Configuration) - See SCS user guide section 2.1 -row 5 - you can limit permissions with custom task to Genral create and delete Computer child objects only.
The other possible cause is that you have not applied SCS 10 hot fix Download Intel® Setup and Configuration Software (Intel® SCS) after applying Microsoft* Security update MS15-096.be used
SCS 9 or earlier can't be used after applying Microsoft* Security update MS15-096.
rgds
darek