Yes - I have had those problems. I have just posted elsewhere about the runtime error issue - where you have to close down Flash Builder and then open and clean before you can go on debugging. I will repeat it again below - in case anyone has a solution....
We cannot delete the swf while debugging after a runtime error in Flash Builder 4.7. This is happening to our whole class and me at home. I have put up with it before because I do not make many runtime errors - but the class does almost every other time they run it. Attached is a screen shot clearly showing that the line the debugger is stuck on is commented out. It seems to be because the swf file cannot be deleted. I am on Windows 8, they are on Windows 7. I spent a day trying to find a solution - I know I can close and clean but obviously, this is not practical. And certainly not practical for beginner Flash Builder coders - especially during an exam.
I will continue to look for solutions. I have tried running as both administrator and not - I have tried reinstalling, it does not matter which version of AIR, it does not matter if it is a trial version or not.
Found a temporary semi-solution. If you get the runtime error the first time then you can look under Run on the top menu and choose Terminate (CTRL F2). Fix the error and then test again. Warning, if you test again before terminating, you are no longer given the chance to terminate and you have to shut down. So... that at least is a way we can proceed without shutting down each time and will do until Adobe makes a fix...
Hey Dan Zen, I am glad to know that I am not the only one working out issues like this.
In my use case I must keep my app running in order to make changes to the app-descriptor xml file at runtime. I am glad that you found this semi-solution.