Hi Mike,
I am not sure what is wrong in your validation process? You are not expected to receive “unprocessed resource” messages for SUPPQUAL domains. Usually such messages are generated when datasets do not have basic SDTM structure. In a case of SUPPQUAL domains you need to ensure that at least QNAM variable is included.
The OpenCDISC tool validates SUPP-- domains as well as SDTM custom domains. You just need to add them into validation list. We highly recommend performing a validation for the whole study data package rather than multiple times by a single dataset.
Kind Regards,
Sergiy