I appear to have answered my own question, but will place it here to hopefully help others.
On comparing another InDesign document that appeared to export to PDF ok, we noticed that the type of frame makes a huge difference to image output quality. In the suspect document the frames with the images in them were " [Basic Graphics Frame]+ ". When I changed the frame (or made a new frame) to " [None] "; not only were the images a lot clearer in the InDesign document but they exported to PDF perfectly. Something so simple!!!!
