There are several ebuilds that depend on their path containing elements like /usr/X11R6/bin and others. Unfortunately /etc/profile unsets the ROOTPATH variable. This variable is used by portage to determine the PATH inside ebuilds.
I found it is actually a portage bug as that is supposed to source profile.env itself
its also been fixed in latest portage releases was a bug with $userland
I'm getting this in 2.0.50_pre10.