Key bindings are disabled/ignored

I’ve recently installed the atom tern-js package (which is supposed to display snippets and suggestions for javascript code) and some of the keystrokes in the package included ctrl-alt-space, ctrl-alt-d and alt-o.

When opening up the Key Binding Resolver (ctrl+period) and testing out these keystrokes, these results all appear the same - with a gray X.

Even though there isn’t another key binding overriding these key bindings, they are still giving out the grey X and no green checkmark.

How should I fix this?

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I had a similar problem, Markdown Table keys not working. I tracked it down to a missing class in the DOM (markdown-table-editor-active) due to the fact that my table was actually not valid Makrdown table. This doesn’t seem to be your case though you could still check whether the expected .platform-darwin|linux|windows class is in the DOM - View - Developer - Toggle Developer Tools, select an element in the page to inspect (using the “arrow in a box” icon in the dev tools). In the Elements tab you see the DOM of the editor pane. In my case I have

...
<body tabindex="-1" class="platform-darwin is-blurred">
 ...
 <atom-text-editor class="editor" data-encoding="utf8" data-grammar="source gfm" tabindex="-1" style="contain: size;">

so the key binding would match. It does not on my machine because the tern selector also contains [data-grammar=~js] but I am in a .md file.

How about creating your own keybinding in the Keymap (keymap.cson) file?
The key combination can link to the atom-ternjs:startCompletion command.