This is an issue with PDFs and eBooks in general. It is not just the Nook, no current ebook reader handles PDFs well.
You see, a PDF is page oriented. It wants specify how an entire page looks. This is why when you view a PDF file on your laptop there are scroll bars on the window.
Ebooks are not page oriented. They want to re-flow the text. Unless your Ebook reader has a screen that is 8.5" x 11", the PDF is going to look terrible.
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