I recently faced myself with a really annoying bug on Flex 3, the “Flex Modules” section of the properties dialog is blank.
After some search on the internet some suggested that it might be a resolution problem. What the f**? So I have to switch resolution to use a program? Adobe Support turned out a dead end so still no permanent fix for this. There is however a small thing you can do, just adjust the divider between the list on the left hand side of the dialog and the right hand content area. Just adjusting the divider a smidge will cause everything to magically appear.
Even though It might seem obvious now it certainly gave me some headaches no being able to add source paths.