On linux only, when the machine is reawakened from sleep, the text in an existing REPL session (or other terminal window) has all or mostly been redrawn in the background color. The sessions are still active, but most new text also comes out in the background color.
Changing to any theme and back again restores all the normal coloring. This is just annoying enough to want to fix, and I don’t understand Atom well enough to know where to look. Any ideas?