Checked, and same problem with Adobe Reader, Adobe Reader Touch and PDF Touch.
I think I already know where the problem comes from.
If you start writing with your stylus on a blank page on OneNote, if your text extends too far to the right side of the page (when writing on an endless kind of page, not a page with a determined size, like A4 size for instance) and then you export it to PDF, you are going to view it as 2 pages, since OneNote automatically divides your text in two different pages, just in case you want to print it down, I guess.
Here you can see and example. I draw a very long wave on and endless page. Once exported to PDF, the very same wave is divided in 3 different pages.
That's what I think is happening to me when I export a PDF from OneNote. As you can see in the following picture of a PDF created by OneNote (viewed with W8 Reader), the original "text" is displaced to the right, it is not perfectly centered. Because of that, when I print a PDF to OneNote, I guess it thinks the whole text doesn’t fit in just one page, so it creates a blank page that follows the one in the picture, just to accommodate the edge of the text of the previous page (there's no such text to be accommodated, since the original text is just slightly displaced to the right, so it still fits perfectly in one page).
So I dare say the problem is that when I print a PDF to OneNote, the program displaces it a little bit to the right, creating a blank page following every written page of the original PDF because it thinks there is not enough space in one single sheet to accommodate the whole text.
What do you think about that? Do you understand what I'm trying to say?