Hyperlinks in Presenter will not work if they are not pointed to an call or another slide in the document. Not sure why you are seeing the call to the doc working. Presenter is intended to be a server based tool, so local file paths are not allowed.
Well, I will assume you are refering to this presentation and it's section on attaching documents through the attachments feature. Is that correct? In that case, the document is actually bundled with the presentation and the download feature will allow users to pull down the attached files from the presentation through the paperclip button on the right of the play bar. Is the issue with that feature, as opposed to the hyperlink functionality?
If that is the functionality you are using, you may want to make sure that it is not a pop-up blocker that is stopping your users from downloading the files, as the download link opens in a new window.
I am referring to Powerpoint Hyperlinking shown in the 3rd Link (Attach Files) or Slide 5 of 8.
Starting at 00:25.
As mentioned in the presentation I added the Hyperlink by typing the name of the file and without including any preceding path. I copied the word and the ppt files to the resources folder after publishing.
After opening the index.htm(offline check) file, the link pointing to the word doc worked fine(it asked to me open or save the file as expected). However, the pptx file link does not even show the hand cursor over the link.
When I pointed both the links to the word doc the hand cursor was active again. So something goes wrong when I am pointing the link to a pptx or ppt file.
The issue I run into is with certain clip art images, the conversion to flash goes badly. This results in the hyper link only working if you carefully mouse over the edge of the image. Text hyperlinks work fine. If you convert images to jpeg and then insert them and add a hyper link it should work. Here is a sample, using the hyperlinking technique shown above, that gives access to a ppt and pptx file, but the center and right clip art image only link on the edge of them.