Have a look at your scope plot. What you see is the chopped current through the stepper, in order to limit the current. But what you see is NOT the current through stepper winding, but the current supplied by the supply voltage, when according MOSFET turns-on! To have a look at current which is flowing through stepper winding, you would need to insert a very small resistance directly into the line running to pin2 or pin5 and measure the voltage drop accross this shunt!

Kai