If you apply hyperlinks to individual objects in a SmartArt Graphic, you may find that they do not link to the correct slide when published with Presenter '09. This is a known issue. You can correct it using one of the following methods:
Use transparent objects to apply hyperlinks
Rather than applying hyperlinks directly to the objects in your SmartArt Graphic, insert PowerPoint shapes to your slide where you want the hyperlinks to appear (on top of the SmartArt Graphic), and apply the appropriate hyperlinks to these shapes. Then remove the shape fill and line color, which will make the shapes invisible.
Hyperlink to the slide after the intended destination
Note: Hyperlinks from a SmartArt Graphic to slides that come before the SmartArt Graphic will always work properly. Therefore, this method only applies when linking to slides that come after the SmartArt Graphic.
Configure your SmartArt Grapic hyperlinks to go to the next slide after the actual destination. For example, if you want to link to slide 5 in your presentation, configure your SmartArt Graphic hyperlink for slide 6 instead. When published with Presenter '09, the hyperlink will direct your users to slide 5.
If you need to hyperlink from a SmartArt Graphic to the last slide in your presentation, you will need to add a slide after the last slide, and link to this new slide. (You can use Slide Properties to hide this slide in your presentation since it does not actually contain any content.)