I just went through this myself and got it working [although not in a RAID configuration]. The problem(s) seem to be related to the system not being able to find the firmware (aic94xx-seq.fw) for the controller at boot time.
Here's what I did to get to working:
First in the Adaptec controller (ctrl-a at boot), delete your raid array so you have two different drives.
Next, boot the ubuntu server 9.10 install disk and install it. After I deleted the RAID array, the install found the drive and I was able to install on the drive but then that install would not boot off the drive.
The problem is that the firmware for the Adaptec 9405w controller doesn't get copied into the initrd image that gets booted when the system starts so it can't bootstrap itself. To fix that, I built a custom initrd image with the required file using the following steps:
After installing, boot the install disk and select "Rescue Mode".
Select the "use /dev/sda1 as root" and select "execute shell in installer environment"
This will drop you in a shell with /dev/sda1 mounted as /target. Now you need to fix up the initrd image on the target to include the firmware you need:
# backup the original...
cp initrd.img-2.6.31-14-server initrd.img-2.6.31-14-server.save
/target/bin/gzip -dc ../initrd.img-2.6.31-14-server | /target/bin/cpio -id
now you will have an unzipped version of the initrd image to which you will copy the firmware:
cp /target/lib/firmware/aic94xx-seq.fw lib/firmware/2.6.31-14-server
Don't put in the adaptec directory like I did at first...
Now you can recreate the initrd image
find . | /target/bin/cpio --quiet --dereference -o -H newc | /target/bin/gzip -9 > ../initrd.img-2.6.31-14-server
reboot and you should now be able to boot the ubuntu server off the hard drive.
There maybe other ways of getting this done, but this worked for me.
Also, you may be able to get this to work with the drives in a RAID configuration but I had problems getting the install disk to recognize the RAID array at all. You might be able to switch to a console window with alt-f2 and rmmod the aic94xx module and then reload it with modprob. I'll leave that to someone else to figure out.
Hope this helps.
Once I got the system up, I found a simple way to ensure that the firmware file automatically gets included in the initrd image if there are any updates to any files in it. I haven't tested this but basically, once you get the os installed and before you do an "apt-get upgrade", do the following:
cp /target/lib/firmware/aic94xx-seq.fw /target/lib/firmware/2.6.31-14-server
/usr/sbin/update-initramfs -k all -u
After that, you should be able to do upgrades with no problem until you get a new kernel.
I tried running update-initramfs from the install disk but ended up wiping out the /target/boot directory so you don't want to do that.