Just to be sure: You did finish calibration and verified the result, and uploaded parameters to the board?
You can not really deduct much from the way the motors run on the ground, you need do a handheld test.. AQ will still have autolevel in "manual" mode, so a better way to verify motor directions is by moving the craft.
In your case you may have a slight level error (or a large one, if the craft is not calibrated), so until the craft senses level, you will see bias in the motors as the attitude controller is trying to correct the error, but has no power (no props) to make it work.
If you have double-checked the motor directions and connections against the mixer table, generated/uploaded/verified calibration data, and made basic setup then you should be ready to make your first hop.
If in doubt you can tie the craft down and make a controlled test like in Mennos PID tuning vid:
http://www.youtube.com/watch?feature=pl ... --fGjodSek