In the /etc/genkernel.conf the options CLEAN="yes" and MRPROPER="yes" both make genkenel run make mrproper after the menuconfig and before the compilition by that destroying all changes made to the genkernel .config by the user. those options should be set to no by default not yes if they even have a reason to exist.
This would be a major change to the way genkernel has behaved for many many years, I'd suggest just setting the options you prefer yourself, or using genkernel's --menuconfig switch rather than editing .config outside of the genkernel process. Please reopen if you'd like to continue pursuing this major change to defaults. Thanks
