I've tried running Atom 1.9.8 on Ubuntu 14.04 as well as LMDE 2 (Betsy) and I'm seeing these same symptoms. I'm only using Ubuntu and LMDE inside VirtualBox and haven't tried Atom non-virtualized. I don't know if that makes a difference. At least Atom 1.4.3 used to work fine in Ubuntu 14.04 inside VirtualBox.
I'm no expert, but I don't think the issue is related to missing Xubuntu/Xfce dependencies, because in Ubuntu, the symptoms are the same in the Unity and Xfce desktops.
In LMDE2/Cinnamon, the black/grey contents of the window stay put on the screen, covering every other window. Minimizing Atom only causes the window frame to disappear.
Sometimes when I close Atom, at least in Ubuntu/Xfce, I get a crash similar to post #4 above.
The --safe and --clear-window-state parameters don't seem to help. I'm getting the black/grey window from a fresh install of Atom.