The problem is specific to the shortcut Control + D. You can change the shortcut to a different key combo and it should work normally. Shift + Control + D works fine, Alt + D works fine, Shift + D works fine, etc.
Upon further inspection, it looks like we have a few shortcuts that are actually hard-coded for the instrument box, which will always override any custom mappings you have. It looks like Control + A is mapped to select all, and Control + D is mapped to select none.
We’ll definitely take a closer look at this. Thanks for reporting.