This may have to do with how the SPDS service is being run (under what account) and which account actually owns some of the files SPDS must read/write. Others might respond with some general SPDS best practices (using the SPDS service accounts as recommended and avoiding use of root, I think), but your particular scenarios might need more investigation with the help of SAS Tech Support.
From the doc:
Regardless of how the SPD Server run-time environment is configured, SPD Server processes always run using the UNIX user ID that started the SPD Server session. That UNIX user ID owns all of the files that the SPD Server process creates. The UNIX user ID is governed by UNIX file access permissions. Remember this when you start SPD Server processes and run SPD Server administrator utilities. Otherwise, it is possible to create files that have ownership and permissions that deny access to required SPD Server processes. If you perform all SPD Server installation and administration tasks from the same UNIX user ID, subsequent use of SPD Server is much easier.