I see. I like top third, so we've always got something above to see where we've just been (and may need to go back to), and visibility of at least part of the next row of pages so you can see how many, if any are ahead. So top third works best for us. I've never used or liked 'top' for the above reasons.
I'm not sure what the program uses as its logic around for deciding the top third. I see "top third" and "middle" works well if you have around 3,3 rows of pages visible. But any less and it doesn't.
I have 2.5 visible rows of pages. Even middle doesn't work for this layout. I would expect with 2.5 rows of visible pages, that top third or middle should keep the active cue in the center vertically always showing part of the bottom row of pages. I can't see how either of those settings should ever force the active cue to be on the bottom visible row. Is there some program logic that's used that needs tweaking? Not trying to be clever, just logical... sort of ;-)