If you have the authoring file and an initial output PDF from this authoring file you could work through isolation of issues in the authoring file.
Most times, for most issues the fault lies in the authoring file.
Another variable is what is providing Tag management.
If FrameMaker, Tag management is good (particularly so for tables).
If InDesign (CS 5.5 or 6)Tag management is good.
If the authoring file is supported by Acrobat's PDFMaker Tag management is good.
If Word 2007, the MS Office 2007 Save As PDF is Tag management ok
If Word 2010, the MS Office 2010 Save As PDF Tag management is good.
Remember that, for Word tables, you must select the table rows that are to be header rows and then select the "Repeat as header row at the tip of each page" property.
The above is predicated on the authoring file's content being mastered properly (in particular tables).
A best practice - when you have the initial Tagged output PDF go into the Tags panel.
Walk down the structure tree to inspect the Table elements for correct semantics.
To look for:
ISO 14289-1 (PDF/UA) - Anticipated to be published / released by ISO this year.
Also anticipated:
PDF/UA-1 Technical Implementation Guide
PDF/UA-1 Technical Implementation Guide: 32000-1
Achieving WCAG 2.0 with PDF/UA (WCAG 2.0 for PDF is PDF/UA)
The last three documents are expected to be available from AIIM's web site.
The four documents, along with ISO 32000-1 (and later ISO 32000-2) are key references for anyone providing accessible PDF.
Be well...