Hi John,
I have this same problem. I have used Multiwii v2.2 and v2.3 and have the same problem. I'm using Turnigy Plush ESC flashed with BLHeli firmware (setup for quadcopter), and Multiwii Pro board with the Atmel2560.
My Quad is flyable, but my PID settings are quite low.
I wonder if this...