The ati-driver ebuild pulls in and builds the xorg-server-1.9.99 as a dependency. If the driver is built after xorg install it breaks xorg all the time as the server is of a lower dependency then the rest of xorg that was built. Reproducible: Always Steps to Reproduce: 1.Install xorg-server or xorg-x11 2.Install the ati-driver ebuild Actual Results: When startx - xorg server crashes and fails to start. Sorry can't remember the exact fault it produces. Expected Results: The dependency tree inside the ebuild should be written with a greater than variable if possible (new to gentoo, don't know if portage would understand a >xorg-server-1.9.99). Only way I know to resolve is to install xorg twice, once with an emerge ati-drivers, then an emerge xorg-(server/x11). Not ideal but it works.
It is not clear to me what is your problem. ati-drivers-11.3 is not compatible with xorg-server-1.10, so you cannot have both installed at the same time. If you have xorg-server-1.10 installed and then install ati-drivers-11.3, portage will downgrade to xorg-server-1.9 first. This is normal and expected.