i have nilfs2 as my root partition also. the only thing that works for me is to call nilfs_cleanerd explicitly as root with no device. so as root i just call "/sbin/nilfs_cleanerd" and it starts on the root partititon. i don't know why this is but it is the only thing that works on my gentoo amd64 system. i would like for it to start at boot but it does not. maybe this will change in the future. good luck.
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