Have you tried

Developer: Toggle Keyboard Shortcuts Troubleshooting

to see what actually gets dispatched?

Hah - turned it off and then it immediately reproduced. Here are some logs.

[2022-02-28 15:16:56.627] [renderer3] [info] [KeybindingService]: / Received  keydown event - modifiers: [ctrl], code: ControlRight, keyCode: 17, key: Control
[2022-02-28 15:16:56.628] [renderer3] [info] [KeybindingService]: | Converted keydown event - modifiers: [ctrl], code: ControlRight, keyCode: 5 ('Ctrl')
[2022-02-28 15:16:56.628] [renderer3] [info] [KeybindingService]: \ Keyboard event cannot be dispatched in keydown phase.
[2022-02-28 15:16:56.961] [renderer3] [info] [KeybindingService]: / Received  keydown event - modifiers: [ctrl], code: KeyD, keyCode: 68, key: d
[2022-02-28 15:16:56.962] [renderer3] [info] [KeybindingService]: | Converted keydown event - modifiers: [ctrl], code: KeyD, keyCode: 34 ('D')
[2022-02-28 15:16:56.963] [renderer3] [info] [KeybindingService]: | Resolving ctrl+[KeyD]
[2022-02-28 15:16:56.964] [renderer3] [info] [KeybindingService]: \ From 3 keybinding entries, matched extension.vim_ctrl+d, when: editorTextFocus && vim.active && vim.use<C-d> && !inDebugRepl, source: user extension vscodevim.vim.
[2022-02-28 15:16:57.470] [renderer3] [info] [KeybindingService]: + Ignoring single modifier ctrl due to it being pressed together with other keys.

Does it happen when Dendron is disabled?

I have never experienced this in any other situation. What's the most useful way to check that? Disable dendron and then try again? Or in a new folder with some markdown files without dendron?

Disabling will do.