1: No I didn't move anything to another drive or partition.
2: Yes, it's set to manual.
OK, I did a little experiment (I wanted to see when the restore points were disappearing):
I created a manual restore point. I immediately checked to see if system restore recorded the point. It did. Well, I was in the middle of doing something, so I decided I'd reboot when I was finished (I assumed the reboot would be what triggered it). I went to check SR again before rebooting (about 20-30mins later) and the point was gone. The computer was never shut off or rebooted and I didn't change anything in the meantime (nothing edited, nothing downloaded, nothing updated). I wonder what's triggering the deletion of these points? They're presumably only retained for about 25min.
This has got to be a clue. No idea how that clue fits into the puzzle, but it seems poignant.