After finding my reading-glasses, I sat down to read the cgpsa documentation, as well as the Communigate docs.
And, found the problem. Nothing to do with SA's cf files (which all were --lint-ing correctly), but rather with the "cgpsa" perl script. It seems it has two modes: (1) "header-only", where the script circumvents the PIPE mechanism, writing its own headers, and (2) "full", where the SA functionality is not tampered with, and headers are touched/written ONLY by SA. The server *was* running in mode (1), now it's running in mode (2). So far, no more MISSING_ or EMTPY_ scores of any kind. I'll wait and see a bit ... but, looks like letting SA do its thing is all that was required. Thanks for the comments. (off to have YA-chat w/ 'Billy' ...)