kernel does not always update using software raid

[mackerel]

I have followed the guide on http://www.gentoo.org/doc/en/gentoo-x86+raid+lvm2-quickinstall.xml to setup raid.
I often have problems after I compile a new kernel with the new kernel not booting. I can see the new kernel when I look in /boot, but after rebooting I still will have the older kernel running. What I do to get by this is to run grub setup again.
grub is set to boot via /boot/vmlinuz and I can verify the times on the files. I am guessing that /dev/sda1 and /dev/sdb1 are not actually syncing as md1 so that one appears at boot and the other appears mounted.

Any ideas one how to fix this?
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Mack