I have a mapping template that contains several embedded Word documents (2003) that each contain a single table. Both in the Word document and in the ArcGIS template (9.3) the text and dot points look fine. However when I convert the template to a PDF, the dot points become squares and large spaces appear between some words in the tables.
That sounds a lot like what happens when you do not embed your fonts within the pdf document. In the export dialog there is a tab that allows you to embed fonts, rasterize graphics, etc. You may need to play around with various settings.
