Thats very similar to what mine was doing as far as running 2 seconds then stopping with a rotor align fault, which the only thing causing it to fail was some drag from the ropes. I also had no success in using the auto align or hf inject stationary alignment methods. It was off by a bit. It would run but poorly.
Are you sure both brakes are lifting fully? Is the encoder cable ran in its own conduit? Possibly a loose encoder connection? It could be a bad part too.
Not sure if it matters much but I'd done a motor auto tune before aligning the encoder also.
Another thing you could try as a last resort would be to go to the U menu and enable encoder alignment then go left or right to the adjust menu and manually change the encoder offset number from what it is after the auto align method. It was roughly 580 after autalign on my car and after the successful open loop alignment it was around 365 just to give you an idea. I doubt that would be the most accurate though.
