I have seen some cases where updates to Windows (2000, XP and server) have turned opportunistic locking back on, even if you had disabled it.

You can check this by running \softrak\system\chksys.exe on both the server and the XP workstations. (The Win 98 stations are not directly affected, but of course are accessing the same files on the server.)

Also, as you point out, a lot of data is moving over the network. That means an unreliable network card, cable or swtich/hub port could be at fault. To isolate this, try copying the data to a local drive and running the same processes. If they run without error locally, the problem may lie with network issues.

(All the best to you as you work to isolate the problem; these intermittent issues can be most frustrating.)