It's been reported a number of times, grimo1re, but I don't think anyone's come up with a direct solution to it.
The closest anyone's come is to format the PDF's 'pages' to the same size as the Reader's display in the first place, crop the margins on the PDF, or run it through something like PDFRasterfarian to chop the pages up so they fit on the display better.
Personally, I just stay away from PDF's, but I understand that that's not an option for everyone.
