IntelliJ IDEA 13.1 is missing Run/Debug windows

Perhaps you have a plugin that is disrupting the execution of the ide?

I had very similar issue today when upgrading from 13.0 to 13.1. None of my gradle tasks were running and the Run/debug windows were not appearing. When I started one of my run targets it froze and did not start until I exited the IDE.

After looking at the idea logs in [userdir]/.IdeaIC13/system/log I found the idea.log riddled with exceptions from the plugin GrepConsole. I probably had an old version of this plugin. To resolve the issue I just uninstalled the plugin using the IDEA plugin uninstall feature. After restarting IDEA 13.1 the IDE is working just fine.

A support request was sent to Intellij on this with these findings:

https://intellij-support.jetbrains.com/requests/24625

and also the author of the GrepConsole plugin was alerted here: http://plugins.jetbrains.com/plugin/7125?pr=phpStorm

For me the windows were simply under "Services". (Alt+8)