Cropped PDFs always scale back to their original size when opened with my Kobo Glo. They are displayed correctly in Adobe Reader, though. My guess was that the original dimensions are still stored in the document. I have no means to verify my assumption, though.
I have no small and free sample at hand, but I can ref a large one: Get the book from http://www-stat.stanford.edu/~tibs/ElemStatLearn/ and crop it (on a Windows machine).
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