Flashing through the firmware recovery tool takes longer than a normal flash - let it sit a good 5-10 minutes when you flash throught that method.
Make sure to also do a factory default reset of the router, by booting with the WPS button pressed.
Thanks will give it one more try following this suggestion. I noticed this thread, which matches the router symptoms, I'd rather not open the device so hope recovery works: https://www.snbforums.com/threads/rt-ac3100-brick.40681/#post-341879