It's a known issue, and I'm not planning on fixing it. Popups disappear when the view loses focus, so the correct fix would be to not allow the popup to display when the view doesn't have focus. However, that would make it impossible to experiment with the popup API from the Console, so I've deliberately left this in.
tgkeul: If your build system isn't showing up in the list of available choices, then (assuming it doesn't have a keyfile setting), it's because it has a selector specified and the selector doesn't match the current scope. You can either resolve this, or better yet, just remove the selector setting in your build file altogether, so the build system is deemed always relevant.
If you've having issues with the build systems changes, it'd be helpful if you could explain what problems you're running into.