It doesn't sound like a PDF encryption or DRM problem, it's just a screwed up PDF file.
Another technique I have used to get a usable ebook from a badly formated PDF is to use the Open Office PDF import feature (requires the optional PDF import plugin), then after fixing anything that needs it, re-exporting the document as HTML and converting to EPUB with Calibre or Sigil (Open Office also now has a promising EPUB export plugin)
But don't be too surprised if this doesn't work.
Some files have interactive java script or other advanced features, that don't work except on the very latest PC versions of Adobe Reader.
In other cases the file is just corrupted.
In yet other cases, nasty folks have even figured out how to embed viruses in PDFs, which normally requires that they intentionally create an internal structure that overruns memory and crashes the reader.
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