Suppose we have a web application named WebApp01. Select it in the Project Explore and execute the Profile menu item. After the application start successfully  job. select WebApp01 and again execute Profile. We'l get a dialog "Profiling  session is currently in progress ... ". Click "Yes" button and quickly click Run button on the next dialog window. As a rule we'l get an "exceptionjava.util.concurrent.RejectedExecutionException: Task java.util.concurrent.ScheduledThreadPoolExecutor$ScheduledFutureTask ...".

The same way the Glassfish behaves. The only workaround is to wait a little after "Yes" answer on the confirmation dialog and before the Run button click (usually we must wait until "Finished building WebApp01 (profile)" message in the status bar of the main window disappears.

I've changed the Tomcatmanager.isRunning method to return true when the current mode is PROFILE and exitValue of the process doesn't throw an exception. This forces NetBeans to call StartServer.stopDeploymentManager. Works nice. The same is true for Nb Google AppEngine  plugin.