x11-libs/qt-core-4.6.0 doesn't depend on x11-libs/libX11 which makes the build fail. This was solved earlier (4.5.3) by patching away this dep, so 4.6.0 should probably be patched the same way. Reproducible: Always
To clarify: the ebuild doesn't DEPEND on libX11, but the ./configure needs it.
This is FIXED, thanks to wired.