I get the boxes when I use the hyperref in my latex documents (I don't
recall every seeing them before gutsy, but so be it). What I found is
that I can tell hyperref not to draw the boxes like so:

\usepackage[pdftex, pdfborderstyle={/S/U/W 0} % this disables the boxes around 
links
            ]{hyperref}

Then pdflatex doesn't put the boxes in the PDF.

(this is a copy of my comment in bug 157073)

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Internal and external links diplay and print problem
https://bugs.launchpad.net/bugs/156643
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