Thanks for making the info/PPTX available. I'll have a look at the EMF + PDF aspect of it later, but for a more immediate workaround ....
>> I also tired the advanced settings options suggested to improve the png quality.
You tried one of the two suggestions I made. The one you missed is the one that's messing up your PNGs. You've pasted the images onto slides with blank content placeholders. If you doubt this, click one of the images, then press DEL to delete it. It'll revert to a blank placeholder. If the image is correctly inserted, it'll disappear, leaving nothing.
When you do this, PowerPoint ignores your compression settings and compresses the images regardless (and for "compresses" read "resamples to lower resolution" or "throws away the information that would have made the PNG look a lot better than it now does").
As I suggested above, if there are any blank content or picture placeholders on the slide, DELETE them, then add your images.