When you "selected all" in the "Photos" section are you sure you didn't have a filter set in the search field (top right of the browser window)? For example it may have been only showing photo's that you had rated when you did the consolidation, so not all photos were selected.
Make sure this box says "Show All" then add a new filter to show only referenced files. Do this by opening the filter HUD (next to the search field box top right of the browser) and select "Add Rule", choose "File Status" then set this to "referenced". This will hopefully give you your 1645 files that you can then select and consolidate.
I have a smart folder of all photo's that shows all the referenced images in my library, it makes checking things like this easy and quick.
Make sure that no filters are set in the search fields (Browser, Inspector) - the searches should show: "all items" or "showing all".
Then create a smart album to show all referenced images:
File -> New -> Smart album
Add a rule: File status is "Referenced"
If any files are shown in the album, consolidate them by selecting only those images from the smart album.
Do a second search with a rule: File Status is "online" or File satus is "Missing", to find stray masters that still are not accounted for.
I discovered last night that immediately after clicking on Photos in LIBRARY, the command changes to "Consolidate Masters for Library...". I used that command and now I think I'm fully consolidated. (As soon as I click in the thumbnails area, the command changes to "Consolidate Masters...".
I believe from googling that the Consolidate Masters for Library might only be relevant to those of us that migrated from iPhoto.
I am now free of referenced masters!