In sys-kernel/genkernel-1.5, doing: * genkernel, then * genkernel --config leaves the second kernel's modules in a possibly broken state, since apparently no make mrproper is done during the build. In my case I was getting modules with undefined symbols when I changed various kernel config options. Doing cd /usr/src/linux; make mrproper fixed the problem.
Will be fixed in 1.6. Thanks! :)