TJ I would look again at what Jamie wrote. In spite of what you are saying I would still go with his gut feeling as to what is causing the problem. It really feels like a sync issue to me. If you don't sync at all but just try manually copying a load of files over and doing some general file transfer stuff I bet you find that no files dissappear, even though there is lots of disk activity going on. If it was drive failure of any sort on this mass scale you would be getting errors reported, certainly in the 323's disk scan.
Running funplug to get some telnet/SSH linux access would be a really good idea right now as it would give you a lot more tools to work with - it's easy to do and you will be glad you did once you try funplug.
I hope you find it - sounds like a very frustrating/worrying error to have.