We've had this problem in RAD 7 with Websphere 7, and it's been an inconsistent nuisance, but we are moving to RAD 9 with Websphere 8.5.5 and it is a MUCH more consistent problem.
What happens is that when starting the application server, it claims to finish starting, but the status from the servers tab doesn't finish, and RAD seems to almost lose conversation with the server. Eventually it reports that the server failed to start within 300 seconds, and tries to stop it, but, having lost communication, it doesn't actually stop.
If you look at Task Manager, in fact, the server did start and is running. The browser talks to the webapps (assuming they were published in a prior session). If you restart RAD, RAD picks up the communication to the server and everything runs fine. But you had to restart to get there.
Under RAD 7, this happened intermittently. Now that we're testing with RAD 9, it happens EVERY time. What's the fix/workaround for this?