Well, I managed to destroy the Supreme score and time databases. I ended up crossing up some scores, so I had to just clear the entire database, since otherwise some unattainable scores would be locked in (I knew something was amiss when 1st place had 250,000 points, and second place had 1000). I'm asking the server guys to restore it from a backup now, something they've done for me before, so it should be no problemo!
The good side of this is that after extensive self-depilation and cranium-to-table interaction, I discovered what the most recent problem with the Supreme scores was, and fixed it. Or at least, I think I fixed it. We'll see! It was amazingly hard to discover. For some reason, the level names now contain a carriage return on the end, and you would be amazed how few methods of viewing data can actually show you a carriage return at the end of a data field. It actually ended up taking a CSV export of the data and then hex-editing the CSV file to see it (couldn't even see it reading the CSV!). And if you don't know what I mean, let's just say it was well hidden.
I'm not sure when that character appeared... it's a recent phenomenon though! Something to do with Vista? Something to do with upgrading my FTP program? Something on the server? Don't axe me, sir. The mysteries of technology.