You're correct, the text inside the scrolling container is getting rasterized at folio creation time, whereas the rest of the text is getting rendered at display time by the PDF engine on the device. This will result in slight differences in appearance on the device, however if you are creating your folios correctly it shouldn't be a sharpness difference.
Are you trying to create content for the new iPad? If so, make sure you are creating your folio in folio builder at 2048x1536. When you add the InDesign document as a PDF article to a folio that size we will rasterize the scrollable frame content at a resolution high enough to look sharp on the new iPad.
Neil
