That's a bug with Repeater being enabled when switching away from a given window.

To minimize the issue:
1. Don't play with Repeater enabled in general -- Key Maps do not exhibit the same issue and do not require Repeater to be enabled
2. If you must play with Repeater enabled in general, you can disable Repeater when switching windows
3. You can use Repeater hotkeys that enable "Current Window" instead of "All Windows"

I need to do more testing on this issue to find the code that causes the bug