I've been having this problem on/off for the last few days:
I start up Eclipse and try to debug my Java Application from the debug button at the top (the bug next to the "play" icon). The application starts, but after a while this pop up is displayed:
If I open the debug view I can see the application and all the threads are running, I can make requests to the application (it's a web server) and it's working fine. But the console view looks like this:
When it should contain a toolbar and have printed some output.
I can stop and restart the application, and the same thing happen. It makes no difference whether I "run" or "debug" the application, or where I start it from (debug menu, debug view, package explorer, F11, etc).
The only way I can fix the problem is to close Eclipse and open it again. It seems to normally work the second time I open it.