Had the same problem but when saving illustrator files to pdfs – it was white text on a magenta background. I could highlight it on the pdf and see it in the preview but not when I viewed the pdf in Reader. Tried numerous things and in the end deleting the offending text (there wasn’t too much) and created text boxes from scratch then it seemed to work. Had used the same font (white out) on several other files and in several other places on the doc but randomly just a handful of bits disappeared in just a couple of the documents.

Alex