For those people out there who are experiencing this cool issue, just upgrade your flash cs4 10.0.0 to 10.0.2. It solved the problem for us.
Sometimes Flash CS4 won’t even show you anything in the Output and/or Compiler errors windows and when debugging your movie it will just tell you that it cannot do anything with a project containing no code or something like that. It is the same issue.
It seems to happen on “very large projects” as the guys at Adobe say but I’v worked on larger project and it didn’t happen. It is a memory related problem and seems to happen when a frame contains too much ActionScript code.
Hope you didn’t throw your computer off the window yet.