Interesting. I hadn't noticed that, but in my Acrobat Pro DC, I have the same issue. I was able to (sort-of) overcome the issue by clicking on the Pages Panel's Options button, and enlarging the thumbnails. Then when I nudged the panel wider, the zoom box then was visible on the thumbnails. A bit odd, but it worked. I would play with this a bit - you might get it to 'stick'.
I hope this is helpful.
I have tried everything. It doesn't always default to the top right but it does always default to the top of the page. I know it worked on Acrobat 8 and Acrobat 9. If you zoom to the bottom left or bottom right corner of one page and then try to make it zoom to the same location on the next page, does it place the zoom window at the top of the new page?
Thanks for the help.
It always defaults to the upper left corner of the page.