You may be suffering from a bug with the pdf library used with Acrobat6 and CS1 apps, where it treats i and l as lines. This is known to happen when you have dashed lines that are not at front (top level) of your layout. can you move any such lines to the front?
This is fixed with CS2 and Acrobat 7.

Another cause may be flattening settings. Make sure your flattening style is set high (say2400dpi) in illustrator's document setup or ID's print or Export settings.
in the case of Freehand 10 the page pallette has an output res set this high then Export as a Macintosh EPS and put this through Distiller.

Try Distiller 5 rather than 6 if you don't have 7.