I've run into the same problem many times, and so far I have just given up and reinstalled. I am running into an issue when I am accessing, either saving to or moving filles from an external usb hdd the internal hdd switched over to read only, then on a restart the system fails to load, I have tried boot-repair in the past and now but it says completed but it does not allow me to boot back into Ubuntu from the hdd, I am currently running it from the live cd. I am tired of this happening, and do not want to reinstall, the issue will occure next time I am reading from or writing to the hdd, it does not happen instantly. At first I thought it was related to the updates, so I tried not updating after a reinstall the error still occure, I thought it was from restarting with the external hdd attached on restart, the error still happened even after safely removing the external hdd. I have tried running sudo update-grub before every restart, this work for about a week, then I was moving backed up files from the external hdd, and the system went to read-only and now once again I can not get back into Ubuntu, the issue happens in 10.04, 11.04, 12.04, and 12.10, I have looking for other options but now I'm getting tired of this happening over and over again. This is on a Toshiba Satellite. And the external hdd is a WD "My Passport" 1 tb.
The line from boot-repair gave me the most recent time was http://paste.ubuntu.com/5694741
Any suggestions or helpful ideas would be much appritiated thank you so much.