Apparently, the site made a formatting change on March 22nd... If you put breaks between your scenes using hyphens/other characters instead of using the horizontal line feature, they're all gone. >:(
From the site:
We do not support dash or other character based section/scene markers. If you wish to create a separation in your chapter, please use the officially supported horizontal line feature in our document editor or in your favorite word program. Using unsupported section markers will only make your entries less compatible to future upgrades. You can create the horizontal lines in Microsoft Word or OpenOffice by typing 3 or 4 consecutive dash/hyphen keys and then hitting enter. The site will correctly recognize these scene breakers when you upload them.
I went and checked -- every doc I have that used that is now messed up. *growls*