Actually, I just rebooted the machine again, and this time it shows the drives and loads the boot rom for the raid controller but comes up with the message "missing operating system ". I guess perhaps the Windows 2003 installed has been corrupted?

Make sure there are no floppies or CD's in the drives.

After enabling RAID, are you able to boot to CTRL-M?

To start with, you might try clearing the NVRAM using the jumpers on the motherboard (you will need to re-enable RAID after doing so).

At this point, assuming your RAID array is healthy, that would appear to be the case.  

Do all the drives show as Online in CTRL-M, Configure, View/Add?  When you go to View/Add, does it ask you to choose between Disk and NVRAM views?  At any point, did you see any message about the RAID configuration?

DonatDonlo,

Is the servers BIOS, ESM/Dfrac, and controller up to date?

Also are the drives hot spare or cabled?

CTRL-M is how you get into the LSI RAID configuration menu.  

Dhris, I pulled the added drives back out, trying to get back to a working system before proceeding. I think the Bios is A05, so it probably needs updating.

How do I get to the point where I ssue the CTRL-M or these other commands? Is it in the LSI Logic Raid configurtion?

Yes Raid is still enabled

If RAID is Enabled but you don't have a CTRL-M prompt, then you have a problem.  If the RAID hardware is malfunctioning, then it will usually disable RAID in the BIOS and/or at least display a message during post as to the problem (memory/battery, hardware missing, etc.).  Remove the entire riser card from the system, disconnect the RAID battery, reseat the RAID memory, reconnect the RAID battery, reinsert the riser card, reseat the RAID key (near the system memory).

I can't seem to execute the CTRL-M command anywhere in the boot process. CTRL-A gets me to the boot order of the raid controller, but gives no option to view the drives...etc...

I did exactly as you advised to the same result. I'll try reinstalling windows Server 2003.