I encountered the same problem as but the solution it proposed didn't work right away. I was adding a flex module to an existing project full of Java modules, and I wondered if that somehow caused the problem. I proceeded to create a new project with a new module and the Flex support worked as advertised. The HelloWorld sample compiled as is -- no need to modify the compiler-config.xml file.
I tried to figure out the difference between the compilation for the new project vs. what I previously had, but the quickly disappearing Message window made it difficult. When I finally managed to get a screenshot of the Message window before it disappeared, I saw that the compiler call in my original project was passing the full path to the source path. According to there are complications with fully qualified paths. What to do!?! It was Intellij that was passing the full path!
I found the solution to be to generate the project contents, IML and source directory, under the same directory as the .IPR file. I usually keep my IPR and IML files away from the actual code directories. I hope JetBrains fixes this limitation for Flex modules -- it's one of the things that Intellij allows for Java that Eclipse doesn't.
Btw, in the end, if your source root is on the same directory as the IPR file, it seems modifying the compiler-config.xml is no longer required. However, if it's on a subdirectory off of the IPR file's directory, then the solution described on might be necessary.