I can try to explain a little better. Let me preface by saying our IT staff figured this one out, not me.
First of all our set up is as follows:
internal server running arcgis for server 10.1.
This is where all our GIS data and services reside (Including the photos we used in our pop-ups)
External Server
Off-site web server running IIS. This machine exists for the sole purpose of running our web map applications. It is connected to our ArcGIS for server installation via the ArcGIS Web Adaptor.
To get our photos to show up we created a virtual directory, In IIS on the web server. This virtual directory was created in the project folder, for our Flex app, running on the public web server. The Virtual directory had a physical path (UNC Share) pointing to the folder containing our photos, on our internal server where we have our ArcGIS for server installation.
We then set the physical path credentials for the virtual directory to a user that had access to the unc share. After creating the virtual path to the photos they began to work in our pop-up.
Hope that helps.