Xserve running 10.4.x reverted to 10.3???

I have an XSERVE that was originally purchased with OS X (10.3) in 2005. Within 6 months, we upgraded to Tiger and have continually kept the software updates up, ending up at 10.4.x.
A few days ago, I had to Remote Desktop in to troubleshoot an issue with MySQL socket errors. I got the standard 10.4 login screen, and tried to fire up both Server Admin and Workgroup Admin (just to review). Trying to open both applications gave me a variation of this error (paraphrased): "Can not run [Server Admin] in this version of Mac OS X."
Thinking there might be an account/privilege problem, I logged out intending to log in as root. As soon as the login screen popped back up, I was surprised to see that it looked like the old 10.3 login window (populated with a list of all account names and icons). I logged in only to find that I could still not run those admin applications.
I logged back out, quitting Remote Desktop to try "clearing" whatever the issue might be, if it wasn't server based. After that point I could no longer see the server showing up as available. It appears as "offline," and returns the Mac OS X version as 10.3. It also returns the IP as 0.0.0.0, even though I can still access the website on that server using the internal 192.168.x.x address, or the external IP address. I can also still mount the shared volumes from networked computers, using AFP and Samba, so it appears to be functional in most ways.
The big issues are:
1) I need to use ARD to troubleshoot the MySQL issue, but do not have any sign that it is possible. I tried name based connections and IP based scanner connections...no luck either way.
2) Why would the OS X version apparently revert from 10.4.x to 10.3? I don't know if this could have been related to low disk space (at that moment 16GB free out of 1.2 TB, which has been remedied to 50GB free temporarily), or if it is something else entirely. I am continually moving data to another volume, so I may be at 150GB+ free later today.
I called Apple Care, but found I have no support contract as of April. However, one tech said reversion to 10.3 was "impossible". Another said he'd never see it, but that an old .plist/config file may be to blame, however, he recommended posting here. Any insight would be greatly appreciated.
Thanks in advance!

No secondary OS on any volumes. I decided to remove the FC card connecting the XSERVE to the XRAID just to pop the video card back into that slot. The machine comes up into 10.3 still, I can't run any server admin items. I started it back up from the install DVD to check what Disk Utilities might reveal.
Apparently I have disk issues on the startup disk (a RAID 5 array). It gets through about 75% of the check before this comes up:
Checking volume bitmap.
Volume Bit Map needs minor repair.
Checking volume information.
Invalid volume free block count.
(It should be 45613367 instead of 45574565)
The volume RAID needs to be repaired.
Error: The underlying task reported failure on exit.
1 HFS volume checked.
Volume needs repair
Running a "Repair Disk" afterward leads to the same result (Error: The underlying task reported failure on exit.) without resolving the problem.
I thought I might take the OS from its 10.3 to Leopard Server, but seeing disk issues makes me think I should take care of this before attempting an upgrade of any kind.
How serious is this, and if Disk Utility can't fix it, is there another way to address the problem?
Thanks.

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