I just went through this thread and as someone had asked, what kind of a torque can your stepper produce at 3 kHz ? Unless this is clocked down further within the drive unit. Anyway that is besides the issue.

To my knowledge most of these stepper drives have opto-isolated control inputs and are specified like this :

Photo-coupler input.
Input impedance 330 Ohm
Input High = 4 to 5.5V ; Low = 0 to 0.5V
( A typical driver from SanyoDenki has this )

So what is the matching specification in your case ?

I dont know if you tried this : Just forget all the ULN2003 , opto stuff. Take a simple Function Generator and with that directly feed the input with 3kHz and with specified amplitude . What happens ?

Some more data needed to tell what is going on.

Raghu