Michael,

i think you are dealing with a known problem which also happened to me a while 
ago. In fact NW will scan everything file but due to whatever reason not feed 
the info to the database. This is for Windows only.

I do not know whether this has been solved in the interim. So my conclusion was 
to send the output fo the process to a log file to anlyze it later.
Then search for the string "index error, flush failed".

If you scan multiple save sets, you will usually not become aware of the 
problem.

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