I think it is the problem of PyCharm.
I have 2 PC with Windows 7 and Windows 10 with French (default) and Russian keyboard layout on both of them. After installing of PyCharm (with 2 weeks interval) an English keyboard layout is appeared on both PCs. And the most surrising is the fact that the Control Panel (Regional Settings -> Keyboard layouts) shows only French and Russian layouts. But if you click on the system tray's icon, you can see 3 of them.
I vaguely remember the question that PyCharm asks me after install, it was something about "non standard keyboard layout". I remember that I allowed PyCharg to manage this fact, but I didn't realize that it will add me a "phantom" layout that I can not remove.
Update: unistalling / reinstalling PyCharm change nothing. But a simple Windows restart removes English keyboard. Till the first launch of my prject from PyCharmm after which a third (English) keyboard layout appears. And I keep this layout even after closing of PyCharm.
Just in case: my python project have nothing to do with keyboard layouts. It's a simple board game simulator, using only mouse to interacte with the player.