You can turn off the auto-build in FB.
The modules are being incrementally compiled and may not be optimized as well.
I turn this off this option and now sometimes still doing the same. Another way to stop this? We are having hard time to compile this project.
Before I post my code to prod server I have to run clean project because the files are huge like I said before but I can live with that.
Well, you can try using an Ant script to build.
I also had a multi-module application, I decided to create a new Flex Project for each module. This way allowed me to work/complile each individually. Probably not using the tools in the best way, but the process is straight forward and quick. Good luck.