I cannot figure out why or how to completely fix it, but atom start at 0,0, which on the Mac is under the tool bar. Therefore I cannot move the window.
The only solution I have at current is delete everything in
~/atom/storage and start reconfiguring my projects. This will work for a little while, but then atom will act up again and I will have to blow away the storage dir to recover.
It seems like it might be due to closing atom if it has a full screen window open, but I cannot figure out how reliably reproduce it.
Atom version 0.123.0
OS version 10.9.4