VSCode Version: 1.20.1
OS Version: Windows 10

Steps to Reproduce:
Open the keyboard shortcuts editor.
Edit one of the default keybinding that generate warning messages and change the combination of keys. For example change with CTRL+SHIFT+I the view explorer keybinding:

{ "command": "workbench.view.explorer", "key": "ctrl+shift+l"},

Expected: No more warning.
Actual: vscode still continues to display the warning messages.

/C:/Program Files/Microsoft VS Code/resources/app/out/vs/workbench/workbench.main.js:1409 Ctrl+Alt+ keybindings should not be used by default under Windows. Offender: e for workbench.view.explorer