When I change the reading order in a PDF (created using InDesign), some images are getting darker. Any idea how to change this back (no, CTRL+Z doesn't work) or prevent it from happening?

On a related topic, my PDF passes the 508 compliance check before I change the reading order, but afterwards the Lists have errors. I cannot figure out how to fix these errors manually.

Thanks!
(Topic originally posted in InDesign forum: http://forums.adobe.com/thread/1351206).