It looks like it's this:
Strangely the releases jump from 2.0.0 to 2.0.3.
I just upgraded to 1.5.3 which seemed to have bricked the Yún board so I had to completely flash everything, voiding my warranty I guess, but on the other hand this Arduino OS seemed like it was really going in the wrong direction and I would have abandoned Arduino altogether if that was the future of the Yun.
I really hope to G~d that Arduino does not pursue this "Desktop" idea for the Yún front-end. It's hideous, bloated and useless. The interface needs to remain clean, aligned with OpenWRT and easily hackable.
Anyway, if someone else has this problem I used the instruction here:
And replaced all the parts: The kernel, the OpenWRT Yun and the U-boot because even the boot loader was Linino.
Now I just have to figure out why the LEDs are not working properly, I guess I'll look into a Yun Shield I have laying around to see if I can replicate the Luci setting for the LEDs.