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I have seen the same problem again an hour ago and used my time to further investigate it. By using the Process Explorer I have seen that when for the file affected there is a sharing violation shown. That means another process still has an handle to that file open. Checking this file via the Explorer has shown that it has a file size of 0 Byte! The last access (modification) time was even 7 days old. Further research revealed that I could use handle (http://technet.microsoft.com/en-us/sysinternals/bb896655.aspx) to show which processes have an handle open to that file. Doing that no other process except javaw.exe is shown. So some class in Jenkins itself seems to keep a handle open.
I think that this can happen to any file within the workspace. I only don't know yet, what triggers the problem. I hope that when any of our jobs fail the next time, the previous job is still in history. That way I could compare times of the last file access and task run at this time.