Chromium and Chrome 48 (just released this week) changed yet again how Chrome Apps deal with window.history, and thus, broke the app. Thanks to a chromebook customer reporting the app not working on a developer channel release, I got a little bit of a head start in finding an environment that would trigger it to happen so I could adapt around it.
The patch was submitted to the Chrome Web Store just now, and should roll out within the hour.
Joe