I just installed 1.2.4 via rpm in my Suse 13.1 Installation.
This error also occurs in the current beta-version.
The Atom-Window is always “on top” and hides everything benath it. Klicking on other windows / switching to other screens will always have the atom window on top.
Only way to minimize it is via the standard minimize controls, but the normal window behavior on loosing focus is not working.