...because I, and I guess many other people, have /usr on a LV...
Hmm. My /usr is on an LV, too. I'll have to check to see if the lvm-user package has changed, but it works for me. Interesting!
Forget it, it was in the middle in the night.. I couldn't think clear. :) The problem wasn't that it was not in /, but that I didn't have a /etc/lvmtab-dir right after the installation so checkfs didn't even try to vgscan/vgchange... Booting the install-cd, mounting root and creating the directory etc/lvmtab fixed it. Maybe /etc/lvmtab should be created by the lvm-utils ebuild?
I have just committed lvm-user 1.0.4 which fixes this bug and bumps the revision. It is *masked* in /usr/portage/profiles/package.mask, so to use it you will have to unmask it. Please do so and tell me how it goes!