Are you flashing userdata.img ? If not, there's your problem. If you are, I don't know. I flashed this Nexus as I did the other one. Same story. No issues if userdata.img is flashed. I bumped into this with my maguro, one time I didn't flash userdata. Bootlooped, straight back into recovery, factory reset straightened it out.
Sent from my Nexus 10 using xda app-developers app