It appears that if the main source folder is deeper than one
level there is a problem in library projects. Here is how to
reproduce the problem.
Create a library project.
Create a sub-directory call "src/flex" and set that as the
main source folder.
Create 2 classes.
Go to the project properties and un-check one of the classes
then click OK.
Now go back to the project properties. Now none of the
classes are checked.
If I go through this scenario with the main source folder
being "src" it all works as expected.