Repro steps:
1. Install the QA provided custom keyboard layout by running "setup.exe"
2. Make sure the installed layout is selected to be used
3. Create a new project
4. Create a GameObject
5. Try to duplicate it using the hotkey according to the custom layout
6. Try other hotkeys like saving, creating a scene, entering and exiting Play Mode, "Flying" in the Scene View

Expected: All hotkeys correspond to the custom layout
Actual: Hotkeys from Preferences -> Keys and some others correspond to a QWERTY layout while some correspond to the custom layout which was selected before the project was opened

Reproducible with: 2017.2.3p4, 2017.4.10f1, 2018.2.6f1, 2018.3.0a10

Notes:
- In some versions, all hotkeys correspond to a standard layout but when trying to type something in the Editor they correspond to the custom layout
- Hotkeys that correspond to the custom and the standard layouts differ from version to version