I think what you are seeing is the way PDFs are created. Some are created with flowable text while others are created as static pages. The difference being, the first can be compared with the text you would see in a word processor while the second would be like pictures viewed in an art program - the first you can adjust, the second is fixed.
There are ways of converting the second type to the first type but if you go to all the trouble then it is better to convert to ePub format.
You could try running the problem PDFs through Calibre and see if that will help.
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