Sorry, this should be working. I haven't tried if for a while, but there have been no changes that should affect this. Can you run calibre in debug mode and posting or PMing the log? From that, I should be able to see what is happening. Debug mode is started by right clicking on the preferences button and selecting "Restart in debug mode". When calibre restarts, it displays a message about debug mode. After connecting the device and the jobs finish, close calibre and the debug log will be displayed.
Also, how are you entering the collection names to be ignored? It should be as a comma separate list of the names.
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