This has been an increasing issue. Every time I open the preferences Atom almost halts my computer (MacPro) to a point that everything stops running. This is probably Atom checking for package updated but, if that’s the case, it must be a more efficient way to do it.
Can you add samples like in this post?
I have a buch of crash logs on Console but im not sure it will help you.
I’ve just tried to reproduce the problem and kept an eye on Console, didn’t show up anything relevant but this time it didn’t halted my machine as often happens.
You can find the logs here: