I found a 2nd definite cause to get an offset to the amount of books.
It is caused as follows: on the upper left part of the Home Page you see a line of previously opened books. A long press on one of those books provides you with options for that book, one of which is the "Remove" option. Selecting that one will present 2 options "Remove from Home" and "Remove from My Books".
I did recently used option "Remove from Home" for 5 books: that "Hides" them from showing on the Home Page, but have them still present in My Books.
However, each time you do this, the My Books count on the Home Page itself is decremented for that "Hidden" book. You won't see that immediately, only when the Home Page is refreshed. So the Kobo FW registers the "Hiding" from just the Home Page as if the book is removed completely from the system. This causes the value on the Home Page to differ from the one on TAB My Books:filter All.
I'm not sure this is a "feature" or a left over from the time that there was only 1 Remove option available: the complete book removal.
By re-selecting all the "Hidden" books, those books appear on the Home Page top again, the My Books value is incremented and is thereafter in sync with the rest of the total book counts.
It took some time, but now I'm also a happy reader again.