Unexpected behaviour when launching Atom from Spotlight

When launching the code editor Atom (atom.io) from Spotlight the spotlight field finds Atom (even when just searching for "a" for example), but rather than showing a list of search options below the search term Spotlight closes after less than a second.

If I immediately press Enter after entering the search term, Atom launches, but if I wait more than 500 ms or so, the Spotlight search term box closes and focus is back on my most recent Application.

I've tested with all other programs in my Applications folder, and Spotlight works as expected with them.

I get the same results from opening Spotlight with both keyboard shortcut (cmd + space) and using the icon in the top right of the top bar in Finder.

This issue started after upgrading to most recent update of El Capitan, a couple of days ago at the time of writing.

I would like to hear if others have experienced similar issues?