Using Office 2016 from Office 365, I was having the same problem with exporting a Powerpoint slide set to Word.
I first had to go into each slide, in notes page view, and reset each page's layout to the current NotesPage settings.
This changed many of my slides to the correct block size, and reset all of my text blocks to the correct size. I used "Ctrl-Y" as a command shortcut to reset each slide's layout, navigating to each slide by using the right scroll bar.
I then adjusted each slide's note block to a font size sufficient to show all of the note text within the Notes Page's note block (and thus not outside the page's boundary).
I then saved this adjusted file.
From there, going into the default view showing the slide miniature images in the left panel, I selected all slides.
From there, I selected File/Export Slides with Notes on bottom. That finally completed the NotesPage handout Word document creation.
I hope this works for you as well.
