After much tinkering, I think I have found what is missing. if you 
update-initramfs -k all -c 
it #warns #W the firmware /lib/firmware/<kernelversion>/aic94xx may be missing, 
sure enough it was in /lib/firmware
I Copied the firmware file to /lib/firmware/kernelversion/ still says its 
missing... Did some more reading... found this may be related to udev rules.

copied:
 /lib/udev/firmware.sh
/lib/udev/rules.d/50-firmware.rules 

into the initramfs img

procedure for adding / removing from initramfs:
mkdir /boot/tmp
cd /boot/tmp
cat <initrd> | gzip -c | cpio -id

/* Add and remove files / edit ... etc... */

cd /boot/tmp
find . | cpio --create --format='newc' | gzip > ../newinitramfs.img
cd /boot
/* backup old initramfs file */
/* rename your initramfs file to the origional in this case it was 
initrd.img-2.6.28-13-server */

I still think this is a bug. as this creates some udev output that I am 
currently unsure how to quiet. 
I found this to be a great learning experience but would not expect people 
trying to get something to work to have to deal with.

Hope this helps someone.

-- 
bug with adaptec aic94xx raid
https://bugs.launchpad.net/bugs/315763
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