noob here reporting same issue and same workaround works for me.

Exact Same issue and hardware and OS as poster. From a clean build, updated all before running MM auto installer as I thought I had made a mistake my first time around.

“used the automatic installer located here, https://github.com/MichMich/MagicMirror, and followed every step.
I’m using a Raspberry Pi 3 Model B.
I’m running Raspian Jesse 4.4, Node v4.4.3.
The MagicMirror is up-to-date”

server nodeonly -works
npm start -does not

changing ‘en’ to ‘’ in config.js works as a workaround. It will now open in electron.