There will be an error between the commanded movement and the actual movement due to inductance and other electrical phenomena. The encoder being on the shaft should have very little following errors though, unless there's a true stall or heavy load.
They appear to be true closed loop steppers, in the manual you can set microsteps ranging from 200-51,200 steps per revolution. They are clearly 1.8° stepper motors, that'd be the only way to get the price point on the physical stepper and controller. The controller uses the encoder as a commutator to close a position loop - in essence you are turning them into a servo, just one with discrete poles.
If your encoders are single ended I strongly recommend going with an encoder with a reference signal - A, A-, B, B-, Z, Z-. The single ended encoders are very susceptible to noise. I know US Digital makes both, but if I had to make a recommendation... these here are a bargain and perform wonderfully:
Omron E6B2 CWZ6C 1000p R abz Encoder Without Losing Pulse | eBay
For the OP:
I would download the protune software
Leadshine Technology Co., Ltd.
Download the manual for the motor - should say "software operational manual"
Leadshine Technology Co., Ltd.
Other closed loop stepper controllers I have seen allow for shaping of the current pulses to the stepper - allowing slight overshoots of the current for very brief periods of time (both are settable). You can essentially squeeze more performance out of a stepper than its rated performance.
It's not clear to me if this closed loop stepper implementation can take advantage of the PPR of the quadrature wave - essentially turning your 1000 points per revolution into 4000 discrete points. It eludes to this, but doesn't say it explicitly.
Things to consider:
Are you wired up correctly?
What kind of amperage is your power supply? It looks like these things can handle up to 6amps.
Do you know your actual torque requirements for your system? A holding torque of 2 Nm (~282oz-in) really is about 70-80% of that in the very low RPM range, then will continue to decrease. Really you're probably at around 225-200oz-in torque in the 100RPM range.
What RPM are you running your steppers at?
Lin Engineering has a great tool in the designers corner that will give you torque curves for your stepper motors based off your power supply. If you're not providing 6amps, it'll give you a good idea of what you're getting (select a comparable nema23 motor to yours)
I did notice in the manual that the position following error is set to 1000 pulses default. I would get the software, adjust this parameter to 4000 pulses.