Wait... bonehead move on my part. I forgot I had ran the update twice by accident so the log I was looking at (for todays date) actually had two complete cycles in it.
In this case, the number of files actually created or modified during the last 12 hours matches the number of entries in the log exactly. So that's the answer.
Also, if I look at distinct directories, I get 1078... exactly the number of "Items" processed by AUSST. So it appears when there are multiple files for a given "Item" they are not included in the count.
Okay, I think I get it now. If you have anything to add, please feel free, but I think I have all I need for my reporting purposes now.
-Brian