Re: [Q] Why do I need to factory reset after flashing stock?
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.
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aosp-maguro READFIRST here (credit: efrant)
aosp-gnex READSECOND here (credit: efrant)