When this happens, does find_under_expand still work the way you expect it to but the file becomes un-editable, or does it just make the file un-editable without having any other visible effect?
Aside of the Default key bindings that provide the defaults and the User bindings that are your own personal customizations, any installed package can also include their own key bindings as well. Your problem sounds suspiciously like an installed package has included its own binding.
You can try copying the default binding from the Default set to your own User set and see if that solves the problem for you. If it does, it’s very likely that you have a package installed that’s doing you favours.
Another possibility is installing the FindKeyConflicts package to search for a conflicting key binding.
In this case you would select FindKeyConflicts: All Key Maps to Quick Panel from the command list, enter ctrl+d (type the text, don’t press the key) and then press enter to be shown a list of all packages that define a binding for that key.
The command will open a buffer that shows you the commands associated with that key, what package is providing the command and in what circumstances the key applies.
For example, on this particular computer the output I get for this command is as follows, which shows that the PlainTasks package also provides a binding for this key, but only for TODO files, and the binding from Default handles everything else.
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Entry Details
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[ctrl+d]
find_under_expand Default
plain_tasks_complete PlainTasks [{"operand": "text.todo", "operator": "equal", "key": "selector"}]