JGcalifornia
If you notice my comment was addressed to dammittakethealias' comment.
Like I said, probably. You do know that reflections, 3D graphs and shadows all use transparency?
You don't have to set it to 72dpi it just does it in certain circumstances.
The quick solution would be to click on my blue name and send me some of the problem pages files and, I gather, the pdf files you have created from them.
Otherwise we can work our way through the possibilities.
1. What resolution are the originals?
2. What format/source are they from?
3. Have you rescaled them up, if so to what resolution?
4. How and what quality have you exported them to?
5. Have you used reduce file size?
Peter