I built an AMD64 system with a bunch of drives that I wanted to setup in a RAID configuration. I partitioned each of the drives with a 128MB boot partition and with another partition that used all of the remaining space. I then setup RAID 1 and RAID 5 on the two partitions using mdadm. I created a LVM physical volume on the RAID 5 partition, created two LVM logical volumes in the LVM physical volume for swap and root and then installed Gentoo. I used dracut to create a initramfs and configured GRUB to first load the initramfs, which then boots the system. Everything works well with one exception. When the system boots, I see "Starting up RAID devices ..." followed by "[!!]" at the right of the succeeding line. I suspect that the init system assumes that the RAID devices need to be configured, attempts to configure them and then throws an error because it cannot configure something that has already been configured.
I also noticed that the system has a few error messages when shutting down. They are on the screen a short period of time, but they say something about "shutting down volume groups [!!]" and then something about 'can't deactivate volume group "vg" with 1 open logical volumes'.
Please paste your `emerge --info' output in a comment.