mount -t ext3 /dev/disk/by-uuid/....failed to mount the correct disk partitions (instead, mounting something other than the uuid partition described in the fstab).
As it is, /dev/disk/by-uuid is populated with relative symbolic links to the referenced partitions, e.g.
/dev/disk/by-uuid/12345-xxxxxx => ../../sda9
What was actually mounted was a similar partition number from a different disk - in my case, for /home, and /local (root partition was - at least - correct).
I updated fstab to point to the raw devices directly (e.g. /dev/sda9, as appropriate). As a defensive measure, I also now version my /boot/grub and /etc spaces (I use mercurial; either git or mercurial would be equally simple).
*sigh*
[update: 5/4/2010]:
It seems there was another casualty of this update (I think): Skype. I only accidentally found out, as I have been using skype since.
However, yesterday, I installed a new computer (and skype on it). Both skype's should work. Quiting skype should log you out of that skype connection. Today, I didn't get any calls on my Ubuntu skype.
I was puzzled at first, but after re-installing skype on Ubuntu, all works as expected. If logged into both, both ring when called. Logging out of one leaves messages in the other.
Since skype-ubuntu worked before re-installing, I expect that something in the libraries that affects sync with the skype server was either broken or severed (the Ubuntu upgrade involved a kernel upgrade). I can't tell what is at fault here, but it is not the first time I've noticed Linux-Skype behavior change, only to be repaired by a skype re-install.
Now, I will treat Skype (along with NVIDIA) as requiring a re-installation (at least, defensively) on kernel upgrades.
