I am not sure what could be the problem. This part had been pretty straight forward for me though. Say if you are creating a new file of about 2MB after a snapshot backup, and when you trigger the next queryChangedDiskAreas call, did you print the Start and lenght of the DiskChangeExtent structure? It should roughly correspond to the 2MB change you made. Other option to try would be to create a child disk to the pervious parent with the returned DiskChangeExtent and see how big the child disk gets.
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