saving to PDF Files are down Sampling raster images for large format printing

I am the Art Director for a large format printing company. We save our files out of Illustrator in PDF format to send to our RIP stations. For some reason in the past month, randomly, files are saving with raster images as very low res images. Most files are vector, and those areas are just fine. But sometimes the raster images that are in the files are saved very low res. I have checked that "DO Not Downsample" is checked. I can save a file and it is perfect, save it again and it is Low res. I am on the most current versions on Adobe. Has anyone else had any simular issues? It is cosing a lot of trouble and reprints.