I tried what Robin2 had suggested for both the horizontal and vertical setups I was using. Both were with motor continuously enabled and drawing a constant current. Motor was in full step mode.
For the horizontal setup following are the readings for various settings.
Error here is more or less acceptable for me.
Confusing part for me is why is it working only in the global enable mode only.
But when I go for the vertical case, errors are very high. So I have feeling the load/torque on the shaft on the vertical motor is causing this issue.
I couldn't do what Paul_KD7HB had told me because, I cant reliably turn the motor by hand by 360 degrees.