This is a copy of the post I made on the Gentoo forums (http://forums.gentoo.org/viewtopic-t-163154.html):
 I've been switching between booting into the Gentoo partition and using coLinux pretty seamlessly for awhile now, but I did the update and got the new baselayout (while booted into Gentoo properly) and things have gotten totally screwy with coLinux now. The method I have been using is the /sbin/rc edit to have it swap fstab's and then editing /etc/inittab to have runlevel 4 point to a special colinux runlevel which did not include things like alsasound, etc. I then have colinux have booting into runlevel 4 in it's bootparams. I made sure to replace the edits I made in both the files after the etc-update, but when I try to load colinux it doesn't appear to be doing the fstab swap anymore. In fact, I tried swapping the fstab to the colinux one manually before rebooting and it appears to be swapping it back. Any ideas?