I know the title may sound stupid, but here it is: I have an ATI video card and an Nvidia video card, and I tend to swap them out from time to time. Sometimes for testing, but usually just in the hopes that the latest fglrx driver won't be totally messed up (ATI's fault, not Gentoo's). Anyway, I have both the nvidia-drivers and ati-drivers packages installed on my system, and when I swap out the cards I just make a minor change to xorg.conf, and run eselect opengl to switch my gl libraries. After updating the ati-drivers package, I found I was unable to use direct rendering with the nvidia driver. It turns out /etc/profile.d/ati-fglrx.sh is setting LD_LIBRARY_PATH to point to the x11 gl libraries, so they would be used regardless of the eselect opengl setting.
Definitely not just nvidia-drivers; this shouldn't install any such thing to /etc/profile.d
I just checked my system. I have ati-drivers installed but I don't have a /etc/profile.d/ati-fglrx.sh file. Could you check that your file is owned by any package? You can use equery from gentoolkit: equery belongs ati-fglrx.sh It could just be an old file left over from some old package that you can just delete.
'equery belongs' does not show it as belonging to any package. I wonder where that file did come from, and why it didn't cause trouble until the most recent update... but it doesn't seem to be Gentoo's problem. I will close this bug with a resolution of INVALID, with an apology for not investigating better before posting.