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have you tried rebooting during the capture before you do the second spy?
have you tried the tools of sysinternals.com, like the filemon or regmon. maybe you can find the process hanging on that file.
if this file is not a part of the application, you can exclude this before you start the spy. or you can explicit exclude it, and copy it manually.
Keep in mind it usually means the file is in use on the host system.
Make sure the program itself is down, you might even have to kill your local antivirus, spyware software etc (anything that might be doing a real time scan).
Generally its either a host service running, the software itself or AV getting in the way of those copies, nothing on the server.
I'd advise against rebooting before taking the delta as you could loose capturing significant pieces like items in the runonce / runonceex keys.