Folders inside a share are randomly disappearing

Hello,
I am having a strange problem with folders randomly disappearing off my server share. Here is my current setup:
XServe running 10.4 connected to 3.5 TB Raid Array via Fiber
Folder inside RAID shared out for client access via AFP and SMB
All clients have automount setup in netinfo.
Clients work fine for about a week, then folders start randomly disappearing. Not files so far, only entire folders. If we try and recreate the folder, it says that the folder already exists, but no one can see it, even if I log in to the server console and access the folders directly on the raid.
I am not very mac savvy, so I am a bit lost as to what I should do next. This would be easier to diagnose if the whole share would become inaccessible, not just pieces.
Anyone have any suggestions?

We just started experience disappearing files. Running Server 10.4.11 (build 8S169). It happens with Autocad files when running Autocad on Parallels. I've been having flaky permission problems on the server, so I am thinking it's time for a (sigh) re-install of the server software.

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Folders inside a share are randomly disappearing

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