Is it one particular NOOKbook you are referring to...? What is the title/EAN? Is this the case with multiple NOOKbooks? If you can supply us with screenshots it would be greatly appreciated.
I was speaking about DRM-free EPUB file which I added to my Nook for PC. But the same thing happens to any NOOKbook as far as I can see.
Now I've just discovered kind of workaround: if a left navigational pane is displayed, narrowing Nook for PC window does actually cause it switch to one-page display mode (nookpc-onepage.png). Hurray!
However, it's enough to hide left pane for Nook to switch back to two-page display mode (nookpc-twopages.png). And application does not allow to narrow window to switch to one-page display mode. It feels like a bug.
Please see attached screenshots.