In the event someone else ends up here via Googling, my reason for a near-full boot volume was a bit of me being a derp.
"/root" lives on the boot volume, so if you FTP as root without changing the home folder and store stuff there, you're storing data on your boot volume. A few ISOs and video files put me there, so in the event that nothing else in this list applies to you and you're running low on space, and you have the habit of FTPing as root (shame on us both), that may well be your culprit.