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First, 'internet archive' PDFs likely are not consistent in conforming to PDF standards. They have probably been generated with a variety of workflows and tools (and perhaps none of them commercial tools, since they have limited funding).
Where there are deviations from spec, PDF renderers don't really have any good options, as there are an infinite number of ways to deviate from spec.
So you may find (as I have in the past) that a PDF generated by OS X cannot be rendered in the then-current version of Adobe Reader, and things like that. You can point fingers, but such inter-operability issues come down to different interpretations of a given PDF spec, or some lack of any quality review as revisions are made.
The analogous issue has lingered for years in browser rendering and even today browsers are expected to handle mal-formed HTML.
Quite possibly your Paperwhite has a different (older) version of the PDF renderer than the Voyage. In improving the software, Amazon may have given precedence to performance (speed, memory usage) and security over handling all sorts of non-conforming PDF code. That would be what I'd expect them to do, and want them to do.
So you have all of these PDF files, and you want to read them on Voyage. I would investigate 'PDF cleaner' or 'analyzer' tools. When targeting small screens and low-power devices like Voyage, it can also help to do some cropping or file size reduction. I don't have any particular recommendations for doing this, but perhaps others will contribute some suggestions here.
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