[Bryany]

This might not be what's causing your problems, but on our robot, the encoder would be missing ticks off and on; it would read for one second, then it would pause, then it would read some more, and so on. The encoder was plugged in all the way, but we found that the problem was because the wire was going into the encoder at an angle. (that the wire coming off at an angle was pulling the encoder out of a proper connection) We taped the wire so that it comes out straight and haven't had any problems since.