On Windows 10, Atom build 1.12.6, when I try to start in normal or safe mode, it becomes unresponsive and asks to close. I uninstalled and reinstalled, same issue.
Try to start Atom using
atom --clear-window-state to see if that solves the problem. You can read about this in the Atom flight manual http://flight-manual.atom.io/hacking-atom/sections/debugging/#clearing-saved-state