Julia,
You've hit a problem I encountered only two days ago. I had been placing Tables into a PM6.5 publication full of Illustrator line diagrams (EPS format) and text. As you noted it wouldnt export a PDF file. I tried one solution (similar to that suggested by viol8ion), and attempted to print to PDF (a shareware program called PrintToPDF) which does a quick and dirty job of outputing a PDF - fine for text but not very good with complex diagrams. However, since PM6.5 exports a nice high-quality PDF, I prefer to get it working if possible. After much fiddling about, I discovered that PM6.5 prefers it if you export the graphics from Adobe Table 3.0 as PICT files rather than EPS. Once I changed this (and fortunately I didnt have too many tables to change!), I could readily export to PDF.
AS an aside, I found that Illustrator eps files seem to work best if exported (for PM6.5)as level 1 postscript rather than level 2 or 3