I assume this only happens with paludis. Installing nvidia-cuda-toolkit-2.1 with paludis will install libraries and binaries in a lib64 directory instead of the intended lib. A simple fix that worked at least in paludis is to add the following line export CONF_LIBDIR_OVERRIDE="lib" in place of the current # don't use lib32 or lib64 directories unset ABI According to the PMS this is indeed the proper way of overriding the library directory. http://dev.gentoo.org/~gentoofan23/pms/eapi-2-approved/pms.html#x1-123001r4
Created attachment 187940 [details, diff] nvidia-toolkit-amd64.patch This one works for me. Brings the ebuild in line with the PMS.
Fixed in CVS, thanks for the patch :)