So the images appear just fine when viewing them via HTML popups in ArcGIS for Desktop, but from the Flex application they don't show up after publishing your map document via ArcGIS for Server? Check to make sure that the account used to run your ArcGIS for Server Windows Service has at least Read access to the directories containing the images (I'm assuming you're using some version of MS Windows operating system). To check this, first open the Windows Services dialog box (services.msc) and double click the ArcGIS for Server service. On the second tab of the dialog box that appears, you should see which account appears as the "Log on as" account. This could likely be a local account called 'arcgis', or it could be Local Service, or some Windows domain account. Next, use Windows Explorer to navigate to the top-most folder containing your images and right click to get to the folder's Properties. Click on the Security tab and scroll through the list to see which local and domain accounts might have access. Does the account running your service appear in the list of accounts with access to the image directory? If not, try adding it (e.g., NT AUTHORITY\LocalService or SERVERNAME\arcgis or DOMAINNAME\arcgisserver, as examples) and assigning Read privileges.
