Hmm, regarding the black loadup screen, that's is an issue I've had before. The very first time I loaded up the campaign, (vanilla NWN, no PRC) I saw the same thing. I restarted, selected premade character and on the second try it loaded up fine.
I'm not sure this will work for you. I think there's some sort of special resource unpacking that is done the first time a campaign is loaded, however, so it's worth just trying again if you haven't. If that doesn't work, I would restore my campaign files to the original .nwms and see if they work. (If that doesn't work, it probably means the gog.com install uses a version of the install that is not 'retail'-equivalent. We can try puzzling over that together, or you might try reinstalling.)
If it resolves the black screen issue, then go ahead and open the PRC Updater and patch the vanilla OC with PRCPack, and then with prc_ocfix, and see if it's still working.
Now, as for the SoU issue, I'm not quite certain why SoU would seem to disappear. Is it not appearing in the PRC Updater? Or is it just not appearing in game? Does it appear in the updater & game, but is it unable to load when you try starting a campaign in it?
Can you get it to work by restoring it to the unmodified .nwms?