I just had this problem yesterday in TurboCNC... For me, it was that I had the parallel port configured incorrectly. The new BOB for the Linistepper drivers that I was working on uses a slightly different pinout than then old one, so it used to be that pin 3 was the direction for the x axis, and now it is pin 6. The program was still set to put the direction signal on pin 3. Once I told TurboCNC to put the direction signal on the right pin, it worked correctly.