Symptom: hyperlinks that worked in a Powerpoint file no longer work in the published Presenter or Powerpoint presentation based on that Powerpoint.
This is because Flash Security treats local content differently than the content on the internet.
The solution is to put the published files onto a web server and access it using the URL (like: http://yoursite.com/yourpresentation.htm).
If you choose to "View Output" after publishing your file, you will be using the file-system path (on Windows, something like: file:///D:/Your Project/yourpresentation.htm) to the content, and even if the files were published directly to a web server over a LAN, you are not actually viewing it through the web.
Here's Adobe's explanation of how the security for local content works:
When Flash Player runs, it performs two main checks before playing the content. If the content doesn't pass these checks, the content is stopped and cannot perform any further action...
During the first check, Flash Player determines whether the content is running locally or on the Internet. If the content is on a website, there is no risk because it is running within a framework that prevents access to your information or local data. If the content is on your local computer or network, Flash Player proceeds to the second check.
During the second check, Flash Player determines if this content is trusted for local playback by checking a list of trusted content stored on your computer. Trusted content is allowed to proceed; content that is not trusted presents a potential risk and is stopped...
--Excerpted from "What is Flash Player security for local content?"
- Adobe Security technote: "What is Flash Player security for local content?"
- Communicate with Internet | Flash Content