To measure the current through my motor controller
Your described circuit measures current to the motor, not motor controller. To measure the current across the motor controller you need to do it between the battery and the controller. Knowing the current to the motor controller is more useful information, since it includes all efficiency losses. Plus, you dont need to account for the motor changing polarity.
And if you need to measure the motor directly . . . Why are you using a differential amplifier? Does your motor reverse polarity? If not, use the non-inverting amplifier schematic.
Looking at the motor controller function table:http://focus.ti.com/docs/prod/folders/print/sn754410.html
It appears that there will always be some
current going across your motor no matter what. If you set EN to low, that should give you a voltage closest to zero.
And a stupid check for the differential amplifier . . . Im sure you did this, but just in case . . . make sure that both R1's and both R2's are exactly the same. For example, with a +/-5% error, your first 10k could actually be 10.5k and the other 9.5k - a 1kohm difference!
if these ideas dont work, let me know and Ill think about it some more . . .