Additional information: I document is 12 pages with 2 charts on each page. I have the 'touch up reading order' option activated. I've also gone through every page, cleared the page structure and then changed each chart back to a figure. I have no tables anywhere in the presentation. Normally, if there is an error found when doing the 508 check, it lists them on the left side of the page. You click on the error and it takes you directly to the error within your document. In this case, I click on the link to the table error and nothing happens whatsoever. It doesn't take me to the page or to a different page when I click on one of the five errors.
You've probably figured this out by now, but just in case:
When you clear page or item structure, Acrobat does NOT always remove the tag. That's what has happened to you- if you walk down the tags structure, you will see your "empty" table tags.
Since there is no corresponding content in the document, the error report link does not work.
In Acrobat 11, they have added a feature to help: you can right-click on the error report and locate the tag! Some types of errors also give you the option of locating in the contents panel as well. Needless to say, this can be a REAL time-saver!!
I work at a college and have to create complex Section 508-compliant PDFs throughout the year. Though you've probably upgraded to CS6 or higher, I thought I'd share info on an ID plug-in that is very helpful with determining and setting the reading order from within ID. It is called "FrameMaker," by Rorohiko, and it puts a tiny label on each frame of a page. For example, if I select a frame, the reading order "number" will show on the top right of the frame. So I'll know immediately that I need to fix the order before creating a pdf.
Very inexpensive. Definitely worth the money.
BTW: If you have to create text files from large ID files, their TextExporter is fabulous.