When building an initramfs, genkernel-3.5.0.6 wrongly modifies the kernel configuration, resulting in a non-bootable initramfs in specific cases. For example, setting CONFIG_BLK_DEV_DM=y gets reverted to =m by genkernel if LVM support is requested in genkernel.conf. In case module copying is not enabled, the initramfs will end up without any LVM support and probably won't boot. Other options are affected as well. This seems to have been introduced in 3.5.0.1 by commit f9324a84, when the sed command was changed so that settings are forced to =m even if they're already enabled.
Fixed in Git: https://gitweb.gentoo.org/proj/genkernel.git/commit/?id=e04962507dee60ce593dd6bb60ed315340056b12