I am trying to see if a newer (read ~x86) release of xorg-x11 helps fix some video problems I'm having and the emerge was failing on media-libs/freeglut-2.4.0 because it couldn't find some GL headers. To fix the problem I manually told portage to emerge mesa and then freeglut compiled fine. The ebuild depends on virtual/opengl but for some reason it didn't work. I don't know if you express an AFTER="virtual/opengl" or something similar but that would reduce headache for people that try the same x11 upgrade I'm trying.
We need to see exact errors. Post them, and also emerge --info output and reopen then.