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New evidence:
I have now seen the problem occur on the command-line twice, i.e. very infrequently, when the backing share is provided by a Windows 2008 server. So it is not just a GUI tool issue, although it occurs almost constantly when we use the GUI tools.
I am in the process of getting the students to migrate their 80 repositories to a share that is hosted on Windows Server 2003 instead of Windows 2008, and to move back to the GUI tools. We will see whether things improve dramatically in the next week or two!
A deeper issue is that if this problem has to do with potential delays or caching in the file system, then John A Meinel's premise in comment #16 - that a small wait loop might solve the symptoms - might be a work-around. But what it really means is that acquiring the lock is not atomic, so we could expect race conditions in which two processes enter the critical section simultaneously. That sounds like a deeper issue ...