The problems you're describing aren't reader or pdf problems, they're really pdf creation problems... a lot of pdfs are improperly constructed by the publisher/producer... they can be fixed, if you know what you're doing, using Adobe Acrobat Pro or any other fully featured pdf editor.
As an example, a recent problem pdf which I looked at, had managed to be made with all the text technically given a hidden attribute. This still allowed reading but screwed up word selection for dictionary use... there are, unfortunately, many other traps for the unwary or "just plain don't care" producers, to fall into... good luck
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