This was a problem a while back and was fixed with an update. It has resurfaced for me.
Atom is open, I click on another program window and then back to Atom. The problem is unresponsive for aprox 5 seconds. It exhibits the same behavior when I start Atom in safe mode (Atom --safe)
It was not doing this on the previous version.
My configuration has remained the same - no new packages installed or deleted, no settings changed
Windows 10 Pro
Atom ver 1.20.0 x64