Energy Saver Preferences resetting themselves

I have an issue with a MacBook Pro Retina 2012 16GB 512GB 10.10.5

I set Energy Preferences to never sleep on Power Adapter, plus disable PowerNap.

Regularly, without me being able to find out the cause, Energy Saver Preferences reset to default settings.

I did SMC and Pram resets several times. Still resetting all by itself.

I did upgrade to Yosemite from 10.9 not so long ago (few months). Surely it didn't do these resets before but I can't say how long after it started.

I am willing to go through troubleshooting to find the culprit but I don't know where to start (what to look for in Console logs etc).

I thought the battery might have an issue. Bit old. But looks ok from Coconut:

Age 1318 days

Loadcyles 345

OS X Battery Status Good

Battery Failure None

Maximum charge 6424 mAh

Design capacity 8460 mAh