When I launch my application in Flash Builder eclipse plug-in, it does not launch the application and comes back with message, timed out compiled with debugger on.
You did not compile your flash app. with the debug compiler
Your project has the wrong server details set up
You don't have a debug version of the Flash player installed
Assuming you used FlashBuilder to build the project the first one is unlikely (unless you also perhaps run an Ant task that uses the mxmlc compiler too?), so I'd check the second.