FYI: I've noticed that Flex Builder 2.0.1 doesn't handle well library dependency in one case:
If you create a Flex Library Project, then create a folder inside of the project, add a library file (swc) inside of the folder and add dependency on the this library in the project properties the Flex Builder would crash. This is new to 2.0.1. Version 2.0 works fine. One way to avoid the problem is so move library file outside of the project folder. More info at: http://stackoverflowexception.blogspot.com/