If /etc/make.profile is directory eix just exists with error: $ eix eix void CascadingProfile::ReadLink(std::string&) const: readlink('/etc/make.profile') failed: Invalid argument It is comfortable to have /etc/make.profile as a directory with only file parents there to include my own profiles from overlays.
Fixed in eix svn trunk (>=eix-0.12.6)
Since eix-0.13.0 is now in the tree, I mark this bug as fixed. Please reopen if the problem re-occurs.