i don't have CS5 so this may be a little different from CS4
but If you are using any raster effects (like illustrators drop shadow) or have a combination of rasters and vectors when you export there is a "transparency" menu that is normally grayed out it will have a box with preset "medium resolution" click the "custom" box beside it and another dialog box will pop up that will have "convert all strokes to outlines" checked... uncheck it.
when a cut contour stroke is converted to outlines it will cut both sides of the stroke that it converted to outlines.