MarjaE -- your post is somewhat confusing. You start out saying that you process PDFs so they can be opened on a kindle, and then you say that Apple has "fixed some of the older problems." How did Apple fix problems involved with displaying a PDF on a non-Apple device (the kindle)? Did you mean Amazon?
Also, depending on what kind of source PDF files you have, they could be re-factored in any number of different ways (convert to OCR, change compression type, etc.). Without knowing what type of source PDFs you are working with and without knowing what specific operations you are doing with PdfGenius or PdfToolKit+, it is difficult to respond to your post. If you want to increase your odds for getting help, maybe you could post an example of the source and the converted PDFs?
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