I've noticed this problem after doing a clean build of all projects (app and libraries) in my workspace. After a clean build, when I launch the application in debug mode, Flash Builder fails to connect to the debugger and is usually stuck with a status of "Launching app: (61%)" for a long time and ultimately reports an error. However, if I just do a clean build of the app (no dependent libraries), I don't have this problem.
This problem also happens frequently after I attempt to run the app from Flah Builder in either debug or non-debug mode after an incremental compile. If I encounter the problem, doing a clean build of just the app will enable the app to be launched.
You may be hitting this infamous issue: http://bugs.adobe.com/jira/browse/FB-16153 (multithreading problem in Flash Player, supposedly fixed now but not released yet). The more CPUs/cores your computer has, the more often you will encounter this issue.