I also take the opportunity to give you a link to one of my other questions that didn't find an answer :

http://forums.adobe.com/thread/439163

I would be glad to have answers from other people than me, because in each of my thread i feel like i'm doing a monologue. Maybe some adobe people ?

For the ones which encountered the same problem as me, I found an other problem in relation with this one.

Sometimes, when you launch an application in debug mode in Flash, even without use of externals swc, the compiler stop on breakpoints, but the little yellow arrow that should appear in this case doesn't. And even if you launch the debug mode again, it doesn't appear. In this case you could think the compiler didn't stop. But at this time, if you open the debug console and do a step by step, the yellow arrow will show and will do it every next time you launch the debug mode.

One tips to be quickly aware of the problem is to drop breakpoints in the constructor of the document class, because the Flash Player won't show before this constructor is fully processed.

I'm back but I have still not found the cause of the problem.

I answered if the fact I work on a server could be the cause, but moving my files to local didn't resolve the problem.

I also have the problem sometimes even without using swc libraries, just with as3 source files.

I even tried to add the breakpoints manually in the Flash's xml debug file but successless.

However, I found a little trick that can be helpful. When the debugger bugs like that, instead of adding breakpoints, I throw Errors, and then the debugger stop on the line where the error is thrown, giving you access to the content of all the variables at that point. But you still cannot use step by step.

Finally I found a solution :

Throw an error in the code and let the debugger catch it, it will open the source file. You can now set breakpoints that will works. Delete the error throwing and the job is done.

PS : During the time I had this problem, I looked for external debuggers on the web. But I didn't found any which could set breakpoints or display the content of private variable cause the most are based on LocalConnection. So if anyone knows a good external debugger...