Banson,
1. That is fairly common for motors running in torque control with no load. I would only expect it to be perfectly flat if you had the motor at stall.
2. In the plot, it isn't showing the Q-axis reference. It is plotting the speed controller output. In torque mode, the Q-axis reference is user.output.drvCommand.statorRefCurrent.q (Q24, BASE_CURRENT). Which should be exactly equal to the value you put in the GUI, stored in user.command.statorRefCurrent.q.
The D-axis reference is plotted against the right axis, which shows it is 0.