I'm pretty sure it's not the ETC now as I've removed the card reader and the windshield sensor.
The beeping is not like any other noise the car makes (attached m4a). It's like a 90s midi mobile phone beep. And always three beeps on start up and every 60-90 seconds. It almost sounds like it's coming from between the head unit and dashboard display.
Beep beep beep.m4a