I've been tagging PDF files for accessibility (Section 508 of the ADA) for over a year. I've encountered all sorts of problems, and found work arounds for a number of them. But I have found NO source of advice or information other than the various Adobe documents, all of which I have read and reread. But they didn't help much beyond the basics.
Many times we are just handed a PDF file and asked to make it accessible -- there is no opportunity to recreate the document in a program that was designed to be compatible with Acrobat or 508-friendly. Using the "make accessible" feature does not always yield results we can use without manual tagging.
Manual tagging may go smoothly or it may not. Sometimes an entire page will refuse to be tagged. Sometimes when an object is tagged an "incorrect PDE object" error message will pop-up. Sometimes when text is manually tagged it will "drop out" of the PDF itself, sometimes it can be found underneath other objects on the page, sometimes not, Any information on these sort of problems would be very helpful.
My latest and greatest problem was with a number 1-page documents created in Word 2000, with heavy graphics, shading and 2-column format text. I tagged 10 such files using a combination of manual and automatic tagging. I had very little problems, I seriously thought things were going quite well! But when I took then to another machine to read them, only 4 would read. Six of them generated a "MSAA tags not present" error. I have never seen this error before. The files could not be resaved on the other machine. Both Acrobat and Jaws crashed in a couple of cases. We prefer to keep our screen reader, Jaws 4.5, on a separate machine because it has it's own display driver which causes problems on our other machines, which we use for page layout and word processing as well as 508ing. These PDFs were tagged in Acrobat 5.05 on a Windows NT machine. They are being read on a Windows 2000 machine. We have Acrobat 6.0 installed but I found it problematic with these particular files because I could not click on and select graphic elements. They were selectable in 5.5 without a problem.
We have active and updated virus protection on all machines.