I had this problem as well every time I exportedmy indesign file to PDF. But after 17 hours sitting in front of my iMac I found a solution which i will share with you.
1. Export you PDF file from Indesign as a usually. 2. Open your PDF file if the file did not opened it automatically after saving it. 3. As your viewing your PDF file on Adobe Reader go toPreview. 4. ThenPreferences 5. PDFand unselect Smooth text and line art. 6. Then just close the image and export it again and you free to go