did some further digging.
So basically it happens only on the Pi3 with dev images.
Also. I stopped using the dev images on both my Pi2 and Pi3
It’s related to this : Disable console over Serial in Dev on RPi3?
And I couldn’t figure out a good solution for it actually to work “stable” just like it does on the prod image. So I’m back at doing lots of comits / git push resin master instead of resin sync.
Serial is too much of a pain to get working properly with the dev images (sorry guys), so prod it is for me.