I'm seeing the same problem.
All of the shortcuts I have configured to go to my FFDL plugin are failing with debug log:
Code:
QAction::eventFilter: Ambiguous shortcut overload: 0
QAction::eventFilter: Ambiguous shortcut overload: 1
QAction::eventFilter: Ambiguous shortcut overload: 3
QAction::eventFilter: Ambiguous shortcut overload: Ctrl+L
QAction::eventFilter: Ambiguous shortcut overload: L
I've used most of these for literally years without conflict and the Keyboard settings under config does not indicate that they are conflicting with anything.
Returning to calibre 2.9, they all work again.