There have been many reports from users as of late suggesting that hyperlinks are failing to operate correctly when publishing PPTX files (PowerPoint 2007 version) to Presenter content.
 
I'll be perfecty honest here...not really sure what the situation is that's causing the problem, and I've seen one instance where hyperlinks have blown apart, but here's a workaround solution that, so far, is working fine, especially for those authoring content in PPT 2007:
 
1) go ahead and create your presentation in PPT, but IMMEDIATELY save it as a PPT (2003) version
 
2) drop in your hyperlinks as usual, making sure that you right click and select Edit hyperlink.  When done, click OK in that dialog box and then publish.
 
3) If hyperlinks already existed in your deck before the PPTX to PPT conversion, you should go back and edit each one individually due to the conversion process.
 
Either way, the hyperlinks should be okay when publishing.
 
Rob