A common problem is to have improper Step/Direction Timing which can cause a drive to sometimes make one step in the wrong direction when the axis reverses direction. Each time this occurs the result is a 2 microstep shift.
I see you have 3.3V TTL output mode selected. Those drives may work better using 5V sinking open collector mode.
Those drives may support CW/CCW mode. Using that mode instead of Step/Direction will completly eliminate any Direction Setup Timing issues.
How to select those modes is described here.