Hello Melinda,
Thank you for your reply. We tried upgrading to PL4, but it turned out that more importantly we needed to forcefully stop any background running processes that were locking certain SAP files.
Basis found that while we had a successfull instalation, some files had not been updated. After a check they found that they were locked by a running process in the backend. Releasing those file on the next instalation helped fix the problem.
Best regards,
Matevz