Hear me, Ubuntu-using brothers and sisters! Never use the on-line upgrade option to switch to a newer version of the operating system! In little more than two years, it has trashed my setup twice, once killing the machine outright, and the last time (yesterday) making it impossible to boot from the linux partition.
When the time comes to upgrade, copy all your files to somewhere else, re-format the linux partition and install the new Ubuntu version from scratch. Then copy all your stuff back onto the partition. There is no safe way to upgrade an existing installation.
A corollary of this is that you should either use an on-line e-mail service that stores your mail off-site, or local e-mail software that makes it really easy to export all your mail to another disk and then re-import it into the software after the upgrade (if any such e-mail software does in fact exist). In other words, do not run Mozilla Thunderbird like I did.