Here are some other things to consider:
Are both encoders giving you identical output? It might be easier to look at the output using System.out.println() rather than SmartDashboard. The output goes to the console in NetBeans, and from my experience is more useful for debugging.
Are you calling Encoder#start() more than once for the encoders? You should only need to call it once at the beginning of the program, unless you stop counting with Encoder#stop(). I don’t know if this would cause the encoder count to reset though.
Have you checked for hardware defects? Ensure that there is nothing wrong with your digital sidecar and cables. As Joe Ross mentioned earlier, the problem you described is often because only one channel of the encoder is being read.
Does your team have any other encoders, such as the US Digital E4P? You could try swapping one out temporarily to see if it behaves any differently. This would help identify it as a hardware or a software issue.