Start by telling us what version of InDesign you are using. Are you using File > Export > Adobe PDF (ID CS4 and earlier) or Adobe PDF (Print) (ID C5/5.5)? What PDF preset are you using?
I am using InDesign CS4.
I am not sure of the next question.
The process I am using to create the pdf file is to go to file>export as you mentioned.
Do the images that don't show in the PDF show n ID when you use Preview Mode?
What colro mode are the images, and are you viewing the PDF in Acrobat, reader, or some other viewer?
Have you set the blending mode of those images to multiply? And as Peter asked: Do you see them in ID.?