XServe RAID firmware upgrade - ASCII identifier

Got called into a situation where files & folders stored on an XServe RAID were disappearing and appearing randomly, not only from the client standpoint, but while looking at the XServe RAID volume on the XServe, as well.
Turned out to be file system corruption that Disk Utility couldn't repair. DiskWarrior seemingly was able to fix it. Ran Disk Utility afterward and it reported no errors. And all the files and folders appear to be there (from the XServe).
However, now the problem is that when a user mounts the main sharepoint, she can only see 15 of the 37 folders. Other sharepoints only show a fraction of the number of "real" folders that should be there. The folders that are missing are at the end of the list alphabetically. Logging in as admin user shows the same behavior.
Redid permissions with Workgroup Manager. No help.
My suspicion is that it may have something to do with the RAID controller firmware. They been running with RAID Admin tools 1.3.2 since it came out, and everything has been fine. However, everywhere I've read emphasizes how important it is it keep the RAID controller firmware updated.
The reason they haven't updated the firmware (to 1.3.2-1.26) is that the Sys Admin there believes that it will mess up the half of the XServe RAID that is serving a Windows 2003 server (his baby). The specific line that terrifies him is:
"- INQUIRY page 0x83 response ASCII Identifier string cleaned up and Identifier EUI-64 replaced with NAA-64"
I just don't have enough server experience to know what that means, nor have my online searches turned up anything.
Can anyone explain what the ramifications of this sentence from the ReadMe are? Is there any reason to suspect that after the firmware upgrade, the Windows server will no longer recognize it's half of the XServe RAID?

Okay, I've solved the problem.
Basically, the issue was that the lower controller wasn't seated right despite it showing a green light in RAID Admin. When I went to visually inspect it, I noticed that despite what RAID Admin 1.5.1 claimed, its light wasn't even on, let alone green. And since the lower controller handles slots 8-14 of an Xserve RAID and my slots 8-14 are totally unpopulated (empty) at the moment, it was never noticed. Now that I've reseated the lower controller, everything is visually showing green across the board and the firmware upgrade is proceeding as expected and it has upgraded the firmware from 1.3.2/1.26a to 1.5.1/1.5.1c complete with autorestart of both upper and lower controller modules.
Basic lesson learned: RAID Admin lies. If possible, visually inspect the box itself!
Thanks to all who responded.

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    Thanks to all who responded.

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