Dear Antonio,
our problem is solved, it seems that there is an issue with installing a new initial system of the SLT with transaction SAINT when you ALSO apply SP 1-4 in the same queue (so installing addon including applying all SP's). There is an OSS note for this which should solve the issue (Note 1830248 - Missing Role NOOP with DMIS 2011 SP4 / DMIS 2010 SP9).
In our case this note was installed but SAP confirmed that in some cases it unfortunately does not solve the issue. SAP connected to our system and manually added some data into tables and after that we could save the configuration again without issue.
So I don't know if you have the same issue but it is recommended when you install a new SLT to just install the SLT addon with SAINT and then apply the SP's manually with transaction SPAM. If you do have the same issue I would recommend to contact SAP and check if they can manually fix it for you.
Kind Regards,
Nico van der Linden