Default [Q] uh-oh. the dreaded bootloop

I was having a few problems with CM11, so I figured I'd start over from stock 4.1.2. flashed (as I have done many times before) via Odin 3.07. On reboot, it went into a boot loop. I never had one before. I re-flashed and got the same result. So, on a hunch, I went into stock recovery, cleared the cache (again) and made a factory reset (again), flashed the root.zip file, flashed CM10.2 and the 4.3 apps, and now it is running.

I'd like to know if anyone can say why the 4.1.2 bootup went into a loop and how to overcome that in the future. I think I might have disconnected from Odin slightly early. It said Reset, but I didn't wait for the beep. Later, I did it again, waited for the beep and now I am back on 4.1.2.