Sometimes you can get a Timeout message or it you could get an error that says
———————————————
C:\WINDOWS\system32\Macromed\Flash\Flash9.ocx

Flex Builder cannot locate the required debug version of the Flash Player. You may need to install the debug version of Flash Player 9.0 or reinstall Flex Builder. Do you want to try to debug with the current version?
———————————————
Even though you have the debugger installed and are 100% sure. The only remedy that i found to this problem is to find where the stand alone player executable is and double click on it. You can find it under Your Flex Installation Directory/Player/TypeofOS/FlashPlayer.exe.  After that close it, return to the Flex IDE hit the debugger and it should work. Make sure to visit the new forums http://vadexFX.com if you have any more questions.