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The focus is lost on some areas of the editor, such as tabs. You can't select different tabs to change documents for example. I can't identify what causes this to happen.
Clicking on another application causes MD to lose focus and then clicking back sometimes resolves the issue causing the tabs to work properly again.
Repro rate: 30%
The version of MD I'm using is the one packaged with Unity 3D ver. 3.5. The MD version is 2.8.2.
It's a gtk issue - newer versions of monodevelop & bundled GTK should fix that.