Seems like it only happens when the keybind is Ctrl + D. My keyboard is EN-US.
I think I've figured out what's going on here. I was fooling around with keybinds a while back and had one of the Create Part Group keybinds set to Ctrl + D. So I'm going to guess that it crashes trying to make a part group with a part that no longer exists.
Another keybind-related issue I've found: clearing the Boost Mode Off keybind doesn't seem to prevent boosted thrusters from toggling off with Ctrl + B. In fact, both the Boost Mode Off and Boost Mode On keybinds seem to do the same thing. I cleared the Boost Mode On keybind and only had Boost Mode Off on Ctrl + B, but boosted thrusters still toggled on when I pressed it.