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I have a similar problem.
The debug mode works with other projects, but on the particular project I'm working on, it does the following:
On first try, it launches the browser but does no debugging. Flex Builder acts like it's running it in normal mode. But, I can no longer build and run the project at all - in either normal or debug mode. I have to close Flex Builder and re-open it to be able to build the project again.
As a note: I too have ExternalInterface in my app. (Although I tried commenting it out, and still have the same problem.)
I was wrong about needing to close Flex Builder 2 - I don't have to do that if I wait long enough for it to time out. It will prompt me with the message saying that it can't connect and to be sure I compiled with debug mode on and have flash debug version installed.
But, it still will not debug, not at all. It will not connect to the application to debug it.
I'm assuming that since my app uses HTTPService, ExternalInterface, and FSCommand, somehow this is interfering with Flash's ability to communicate with Flex Builder. I will experiment and report on my findings.
I figured out MY problem...
I edited the html-template file index.template.html and the debugger needs the default code to work correctly.
I changed it to use ufo.js to insert the flash content instead of the default AC_OETags.js file, which I guess is required to make the debugger work.
The one thing that is kinda bad, is that if Flex Builder can't connect to the flex app, it just sits there and does nothing - and you can't build the app again until it times out, or you close FB, whichever comes first. I think that either the timeout should be shorter, or you should be able to cancel it somehow.
U can cancel the launch in the "progress" panel. At the right end side is a little red square, when u click it the launch cancels.
For me, i haven't done anything with the -debug.html file myself. I can launch the debug session, the site appears in my browser, and i can operate the site. But in the flex application, the connection cannot be made.
For some compiles, the process window does not show up - only a message box telling you that flex is doing something - and even the cancel button is grayed out. I don't know specifically which actions cause only this window to appear instead of the other one with the processes.
Also, I think the file you are referring to is the one created AFTER the compile. I believe that there is only one index.template.html file - and it is located in the html-template folder of your project folder. Correct me if I am wrong.