I'm on the latest release version (not nightly); I'm just wondering whether there could be a bug in the nightly? Perhaps try using the updater to install the latest release version and try again.
Well, as far as you know it is. It's possible there's an area of corruption which can't be written to and that happens to be where the update is being saved to. Like I said, if you don't have another SD card to use, you could try running a tester on it. Also you could copy the files off, format the SD card, and copy your files back.