The following error only occurs in closed loop systems. It is simply the difference, in counts, between the commanded trajectory position and the actual feedback position. A good way to characterize your following error is to go into the Advanced menu of the 1-D Interactive portion of MAX, run your motors at a very low velocty (1 rpm), and watch the Following Error indicator. If it is increasing slow and steady, then you probably have the encoder resolution wrong. If it jumps up in spurts, then the encoder may be damaged. If it is increasing very fast, then either the encdoder isn't plugged in, the encoder isn't working at all, or the encoder is plugged in backwards.
I hope this helps.
Kyle V
Applications Engineer
National Instruments
www.ni.com/ask